Thank you for your reply!
Come to think of it though (and despite my question), considering the way the add-on is currently set up, I think it makes more sense to let both run at the same time.
What would be great however, is if the user could save and load sets of replacements. Then, both the regular and the regex replacements could be integrated into the same window, with an additional checkbox specifying whether the replacements of that set should be interpreted as a regular or a regex replacement. That way, if a user wanted to perform different replacements, he could simply load a different set. I realize though, that it would probably require a lot of work to implement this and maybe more than you quite understandably can or want to devote.