One of the best-known examples of a work of art being modified against the wishes of the artist is Michelangelo's "The Last Judgment." From the moment it was first seen, the nudity of the figures was controversial, and after the Council of Trent decreed (twenty-some years later) that "nothing that is profane, nothing indecorous," was to be placed in a church, various draperies were added to cover the more indecorous elements.
Nowadays, Michelangelo is generally held to have been right, and efforts have been made to restore the work to its original form. We snicker at the prudishness of those sixteenth century philistines (one of whom wound up immortalized in the lower part of the painting).
But, really, why do we think Michelangelo was right? On what do we base our judgment? My guess is that everyone's reasons can be looked at as based in part on particulars, in part on principles, and in part on prejudices.
A particular reason would hold that, in this case, the nudity happens to be better than the drapery, that for this fresco on this wall in this chapel, Michelangelo's version is superior. It may be "better" or "superior" because it's a better work of art, or even simply because Michelangelo was a better artist than those who followed him, and the more we can experience his vision the better.
The prejudices are obvious and can be expressed in either particular (e.g., "Michelangelo knows best") or general ("Prudes are losers") terms.
What I'm really interested in are the general principles that might be proposed for thinking Michelangelo was right. This is, I think, something of a stressing situation: it's a commissioned work, so the artist isn't free to do absolutely anything, nor does he own it afterwards; it's a fresco, so it can't be moved; it's for a chapel, so it can't be profane or indecorous; it's for a pope, which raises unique concerns for scandal.