I'm leaning towards either asking the user what to do, or to just use the last write as the winner and not worry about it.

If you're going to ask the user, you'll have to make a UI where the user can edit the conflict. You may want to have a look at various wikis, who have to deal with this as well.

If the last write is going to be a winner, just use git, with something like git merge -s recursive -X ours. (Or -X theirs, depending on which way you're merging).