Wow, I'm quite flattered that people are into Penlight enough that they're basically writing fanfic about it ^.^ But ehh, yeah you've already identified the problem with this: You don't have a way to distribute it as a mod without also packaging the rest of the game with it, and I'm a bit iffy about that for the same reasons you cite. If there were a way to distribute just the modified script as some kind of fan-made patch, that'd be one thing, but yeah, I'm not comfortable sanctioning a derivative version of my game. Even done with good intentions it's going to muddy the waters a bit.
So, not against modding in principle, but unless there's a way of doing this without redistributing the entire game I'd ask that you refrain from doing that.