Except for the word “harvest”, the line is not difficult. “Thou” is the addressee of the ode, that is, the “Comic Spirit”, a phrase peculiar to Meredith, by which he means clear-sighted apperception and gentle ridicule of human folly. In his essay ‘On the Idea of Comedy’ (1877) he explained the concept thus:
If you believe that our civilization is founded in common-sense (and it is the first condition of sanity to believe it), you will, when contemplating men, discern a Spirit overhead; not more heavenly than the light flashed upward from glassy surfaces, but luminous and watchful; never shooting beyond them, nor lagging in the rear; so closely attached to them that it may be taken for a slavish reflex, until its features are studied. […] Men’s future upon earth does not attract it [the Comic Spirit]; their honesty and shapeliness in the present does; and whenever they wax out of proportion, overblown, affected, pretentious, bombastical, hypocritical, pedantic, fantastically delicate; whenever it sees them self-deceived or hoodwinked, given to run riot in idolatries, drifting into vanities, congregating in absurdities, planning short sightedly, plotting dementedly; whenever they are at variance with their professions, and violate the unwritten but perceptible laws binding them in consideration one to another; whenever they offend sound reason, fair justice; are false in humility or mined with conceit, individually, or in the bulk—the Spirit overhead will look humanely malign and cast an oblique light on them, followed by volleys of silvery laughter. That is the Comic Spirit.
George Meredith (1877). ‘On the Idea of Comedy and of the Uses of the Comic Spirit’. In The New Quarterly Magazine (April 1877). Reprinted (1897) in An Essay on Comedy and the Uses of the Comic Spirit, pp. 88–90. Westminster: Archibald Constable.
In the ode, the Comic Spirit is the “issue” (meaning offspring or product) “of the brain” because it is a product of human culture, and it is a “guardian” because it defends society from the “affected, pretentious, bombastical, hypocritical, pedantic” and so on, by ridiculing them. Hence Meredith gives it the epithet “sword of Common Sense” in the first line of the ode.
This leaves us with “harvest”. I have two suggestions. The first is that Meredith uses this as an adjective with a meaning along the lines of “ripe, mature, ready to be harvested”. The problem is that the required sense does not appear in dictionaries (I consulted the Oxford English Dictionary, Merriam–Webster and Chambers). However, the word does appear in something like this sense in the phrase “harvest-field”:
harvest-field, n. A field in which the corn is being reaped or gathered in; a cornfield in harvest.
Oxford English Dictionary.
And so it is not unreasonable for a poet to analyze this phrase and recover an adjective “harvest” meaning, “in the process of being harvested”.
My second suggestion is that Meredith is using hypallage, a rhetorical device in which “a modifier is syntactically linked to an item other than the one that it modifies semantically” (Wikipedia). Under this suggestion, the line means “Thou guardian issue, harvest of the brain” (where “harvest” is synonymous with “issue”), but the modifier “harvest” has been transferred from the item it properly modifies (“Thou”, meaning the Comic Spirit) to another (“brain”).
The two suggestions are not mutually exclusive: the compressed language of poetry often generates ambiguities of phrasing, the multiple senses of which all contribute to the overall effect.
P.S. The “anomalous extra white space” that the question expresses some concern about is just a typographical convention and has no particular significance. This convention was very common up to the mid-20th century, for example, in 1954, a typographical manual advised, “Spaces are used before some punctuation points, such as question marks, etc. Thin spaces are placed before colons, interrogations, semi-colons, or exclamations, when these follow a word.” (John Southward, Modern Printing: The Practice and Principles of Typography and the Auxiliary Arts, volume 1, p. 179.) This convention was mostly superseded over the second half of the 20th century by the modern convention in which there is no additional space in these positions.