I'm already working on some scripts to manage my file system, and sync it to a repository. One of my goals is to, when syncing fails due to .tid files needing to be merged, it will wrap the .tid files in question in another temporary .tid file, where you can merge tiddlers from within the web interface, and request a push.
I do think that relying on an external revision/conflict management system like git could be a great path forward.
One problem with merging for conflict resolution, as you requested, is what to do if the tiddlers contain more than just text. Should the. Headers be merged?