To understand the meaning of Stanza Three in this amazing poem you need to understand what has already been established in Stanzas One and Two. In these first two stanzas, the speaker is encouraging his wife to not mourn his death loudly and urges her to part from him quietly, because it would spoil the sacredness of their love to display their feelings publicly:
'Twere profanation of our joys
To tell the laity our love.
To somehow reveal in a very overt fashion the deep feelings they have for one another in front of other people would lessen or cheapen the love that they had, and thus it is far better to part quietly and not to mourn openly.
Thus in Stanza Three the poet continues to offer proof for what he wants his wife to do:
Moving of th'earth brings harms and fears,
Men reckon what it did and meant,
But trepidation of the spheres,
Though greater far, is innocent.
When an earthquake occurs, men constantly ask what does it mean or what does it point towards. However, irregularities in the movements of remote heavenly bodies is a far greater natural disruption yet it is unobserved and harmless compared with earthquakes.
Thus the author is encouraging his wife to be like the heavenly bodies - his death, he knows will be incredibly significant and hard for her to handle, yet by allowing her grief to go unobserved and not mourning she will ensure that this tragic event will be of far greater significance than an "earthquake" which is not as seismic an event as irregularities in the movements of planets and stars.
The metaphor of stanza three refers to parting and disruptions: Earthquakes destroy earth and the dwellings on it. Trepidation of the spheres disrupts the smooth, circular movements of heavenly bodies. Both these metaphorical equations may be considered less harmful than the parting of lovers because they are distant, inanimate, and nonfeeling. To pursue the metaphors, however, we may conclude that these cosmic movements do no permanent harm, and that they are therefore “innocent.” How, in comparison, can the less cosmological parting of lovers do any harm?