The problem is really with how comments get ranked. Reddit comment threads annoy (some) people because "easy" jokes float to the top, when what (those) people really wanted to see is direct, charitable engagement with the parent post/comment.
Also, a joke subthread can often have a sort of "gravitational force" that engages people in replying to it such that they never end up contributing to the "real" discussion happening below it, because they never make it there. This effect gets worse the earlier in the comments the joke appears. (This also happens with political tangent-subthreads, but nobody likes those.)
I think (these) people would not be made nearly as upset by jokes if they didn't "interrupt" the flow of conversation by appearing first in comment-subthread-ranking. I'm not sure how that could be done without manual moderation, though; people will always want to reward jokes with points, because jokes do have genuine utility to their consumers. They just can choke out the production of more serious worthwhile sibling contributions.