From Deborah Grosvenor, Grosvenor Literary Agency:
I always get involved when there is a jacket issue. This can be an emotional issue for writers. They want to be proud of the book they are holding up with their name on it. As one editor once said to me, a bad jacket for an author is like a blemish that appears on a teenager's chin right before the prom. No one else notices, but it's all that they can think of.
I find that the most effective way to get a jacket changed is for me to convey an author's heartfelt objections to the publisher in a reasonable way. In most instances, the publisher will respond with some form of change. In one case, however, we'd reached a complete impasse, with the publisher refusing to change their preferred jacket in any way, and my client refusing to be associated with the book if they moved forward with their jacket. It finally took a meeting between me and the editor-in-chief and publisher to present my client's case, as well as my client expressing his obvious distress directly to the editor, to get them to change the jacket.
So, yes, authors should always feel they can call on their agent to intervene when there is a serious jacket issue.