The "jewel of the secret treasury" strikes me as the heart, and the "seal" and "key" refer to the heart being preserved for the lover and loved, while the "pearls" refer to the loving glances between.
Hearts are often referred to as jewels in poetry, and we also read of the "seal" being upon the "treasure casket"; as the heart is a "jewel", this implies it being a treasure, and thus implies the seal being upon the heart; the key, mentioned in the same line, therefore unlocks the seal. This sort of preservation of the heart for each other, and pure romantic love, is indeed something thieves "can neither break nor steal", and the seal and key further imply the "loyalty" that "still among lovers is found". Later in the poem, too, we see the reference to the blood of the heart and rubies, further implying the jewel of the secret treasury is the heart.
Finally we come to the pearls; this I find a little more difficult to interpret. However, when I first looked at the poem my thoughts went to the glances you see lovers give each other. You can spot people in love by the way they look at each other, and I think that this poem is also implying that by looking at the ground you are not looking at anyone else in that way ("faithful eyes" and "loyalty [among lovers]"; italics my own). We also see in a later line the reference to "a dart from thy bent brows has wounded me" implying the angry glance wounding, which is in contrast to the pearls, or faithful glances, rewarding.
The poem is thus setting up the love of the two, and how the speaker's heart is still saved for the other, while the second stanza sets up the argument the loved has with lover, and the lover's wait even still for her to come back, and then the third stanza talks again of his heart and lips (both remind one of blood-red rubies) and how they are still saved, and how he will not hide or forget his love ("Would'st hide the stain / Of my heart's blood?"), and then finally the fourth and final stanza talks of the loved's rule, almost cruel now, over his heart, as he still has not gotten over his love.