TL;DR: No.
Censorship
Until the second half of the 20th century, it was not easy to publish literature in English that described sex in detailed or explicit terms. In England, literature was censored according to the Obscene Publications Act 1857; and in the U.S. according to the Comstock laws. These laws, prosecuted by private organizations like the National Vigilance Association in England, and the New York Society for the Suppression of Vice, made it necessary for mainstream writers like Conrad to approach sex obliquely, using implication, ellipsis, allusion and symbolism in place of explicit description.
This code relied on a common understanding between writers and readers of what was permissible to say and what could plausibly be read into the gaps. But sixty years after R. v. Penguin Books Ltd and Roth v. United States it can be hard to accurately reconstruct what the original audience would have understood from a work, and easy to miss some implications and read too much into others.
Evidence
Conrad’s ‘The Duel’ is a fictional account of a real rivalry between two cavalry officers in Napoleonic France. ‘Feraud’ represents François Fournier-Sarlovèze, known as ‘Napoleon’s Devil’ and ‘the worst subject of the Grande Armée’ for his duelling, fraud, political conspiracy, dishonesty and other crimes. ‘D’Hubert’ represents Pierre Dupont de l'Étang, whose only brush with the law seems to have been his court-martial for surrendering at Bailén in 1808. Thus, rape might be in character for Feraud, but not for D’Hubert.
‘The Duel’ was published in 1908. Based on comparable passages in contemporary works (see below for details), readers of mainstream fiction in this period would not have been expected to deduce a rape or attempted rape merely from the hint of “manifesting his gratitude in an aggressive way”. It seems more likely that a less serious sexual assault, such as a kiss, is intended.
The maid is not alone in the house: there is a landlady and at least one more servant, a gardener (who is deaf, but D’Hubert would not know that):
“And if you want any witnesses, I’ll send word to the old girl to put her head out of a window at the back. Stay! There’s the gardener. He’ll do. He’s as deaf as a post, but he has two eyes in his head.”
A subsequent interaction with the maid suggests that she is scared of Feraud but not of D’Hubert:
The pretty maid had opened the door. Lieut. Feraud brushed past her brusquely, and she raised her scared and questioning eyes to Lieut. D’Hubert, who could do nothing but shrug his shoulders slightly as he followed with marked reluctance.
Compare the brief clause “which at first was repulsed violently” with the detailed description of the maid’s behaviour after the first duel, when she mistakenly believes that D’Hubert intends to kill the wounded Feraud:
The affair was ugly enough as it stood, and Lieut. D’Hubert addressed himself at once to the task of stopping the bleeding. In this task it was his fate to be ridiculously impeded by the pretty maid. Rending the air with screams of horror, she attacked him from behind and, twining her fingers in his hair, tugged back at his head. Why she should choose to hinder him at this precise moment he could not in the least understand. He did not try. It was all like a very wicked and harassing dream. Twice to save himself from being pulled over he had to rise and fling her off. He did this stoically, without a word, kneeling down again at once to go on with his work. But the third time, his work being done, he seized her and held her arms pinned to her body. Her cap was half off, her face was red, her eyes blazed with crazy boldness. He looked mildly into them while she called him a wretch, a traitor, and a murderer many times in succession.
If the reader were expected to believe that D’Hubert raped the maid, then surely Conrad would have written a description more like this one.
The first part of ‘The Duel’ is set in Strasbourg in “a short interval of peace”. A cavalry officer might be reckless about rape in enemy territory during wartime, but it was a different matter in a city in peacetime France where he would risk discovery and court-martial. In particular, after the maid attacks D’Hubert he is worried for his reputation:
This did not annoy him so much as the conviction that she had managed to scratch his face abundantly. Ridicule would be added to the scandal of the story. He imagined the adorned tale making its way through the garrison of the town, through the whole army on the frontier, with every possible distortion of motive and sentiment and circumstance, spreading a doubt upon the sanity of his conduct and the distinction of his taste even to the very ears of his honourable family.
Comparison
To try to understand what readers might have expected to encounter, here are some passages describing rapes and attempted rapes in works approximately contemporary with ‘The Duel’.
In The Man of Property (1906) by John Galsworthy, Irene Forsyte refuses consent to her husband Soames:
He answered: “I want to know how long this state of things between us is to last? I have put up with it long enough.”
“Will you please leave my room?”
“Will you treat me as your husband?”
“No.”
“Then, I shall take steps to make you.”
“Do!”
And then a couple of chapters later he rapes her:
The morning after a certain night on which Soames at last asserted his rights and acted like a man, he breakfasted alone.
He breakfasted by gaslight, the fog of late November wrapping the town as in some monstrous blanket till the trees of the Square even were barely visible from the dining-room window.
He ate steadily, but at times a sensation as though he could not swallow attacked him. Had he been right to yield to his overmastering hunger of the night before, and break down the resistance which he had suffered now too long from this woman who was his lawful and solemnly constituted helpmate?
He was strangely haunted by the recollection of her face, from before which, to soothe her, he had tried to pull her hands—of her terrible smothered sobbing, the like of which he had never heard, and still seemed to hear; and he was still haunted by the odd, intolerable feeling of remorse and shame he had felt, as he stood looking at her by the flame of the single candle, before silently slinking away.
In Ann Veronica (1909) by H. G. Wells, the newspaper proprietor Ramage attempts to rape the heroine after a dinner but she resists him:
Then before she could say a word to arrest him he was at her side. “Don’t!” she said, weakly, as he had bent down and put one arm about her and seized her hands with his disengaged hand and kissed her—kissed her almost upon her lips. He seemed to do ten things before she could think to do one, to leap upon her and take possession.
Ann Veronica’s universe, which had never been altogether so respectful to her as she could have wished, gave a shout and whirled head over heels. Everything in the world had changed for her. If hate could kill, Ramage would have been killed by a flash of hate. “Mr. Ramage!” she cried, and struggled to her feet.
“My darling!” he said, clasping her resolutely in his arms, “my dearest!”
“Mr. Ramage!” she began, and his mouth sealed hers and his breath was mixed with her breath. Her eye met his four inches away, and his was glaring, immense, and full of resolution, a stupendous monster of an eye.
She shut her lips hard, her jaw hardened, and she set herself to struggle with him. She wrenched her head away from his grip and got her arm between his chest and hers. They began to wrestle fiercely. Each became frightfully aware of the other as a plastic energetic body, of the strong muscles of neck against cheek, of hands gripping shoulder-blade and waist. “How dare you!” she panted, with her world screaming and grimacing insult at her. “How dare you!”
In The Sheik (1919) by E. M. Hull, Sheik Ahmed Ben Hassan abducts and rapes the heroine Diana Mayo:
The warm sunshine was flooding the tent when Diana awoke from the deep sleep of exhaustion that had been almost insensibility, awoke to immediate and complete remembrance. One quick, fearful glance around the big room assured her that she was alone. She sat up slowly, her eyes shadowy with pain, looking listlessly at the luxurious appointments of the tent. She looked dry-eyed, she had no tears left. They had all been expended when she had grovelled at his feet imploring the mercy he had not accorded her. She had fought until the unequal struggle had left her exhausted and helpless in his arms, until her whole body was one agonised ache from the brutal hands that forced her to compliance, until her courageous spirit was crushed by the realisation of her own powerlessness, and by the strange fear that the man himself had awakened in her, which had driven her at last moaning to her knees. And the recollection of her abject prayers and weeping supplications filled her with a burning shame. She loathed herself with bitter contempt. Her courage had broken down; even her pride had failed her.
Without claiming that this is any kind of definitive survey of the period, I note that although in these passages the reader has to do some imaginative reconstruction, the essential facts of what has happened are clear and the reader isn’t left in any doubt as to whether rape has or hasn’t occurred.