As a side note, it would be really useful if there was some way of quoting context that didn't trivially lend itself to forging context... (though admittedly that's a much smaller problem).
Simple solution: store the comment revisions, and when you go to a reply, allow the user to see the revision that was active when the reply was posted.
Simpler solution: Leave things the way they are. It doesn't make sense to dramatically increase your storage costs and UI complexity over a feature 99% of your users don't care about and a substantial number will actually be annoyed by.