I think it would be ideal if script like that would be run by Stack Exchange automatically and feed it into a dedicated review queue where hundreds or thousands of reviewers would validate the results.
Another option is to set up a dedicated chat room and feed links to comments discovered by a script into it, for attention of users interested in cleaning up. This would be pretty much similar to the way how "SO Close Vote Reviewers" run and coordinate their efforts.
Have to admit, current way feels quite awkward. Diamond moderators, "human exception handlers", carefully picked and elected experienced users, assumed smart and credible enough to evaluate really tricky cases, are forced to decide whether "+1 thank you" comment is to be deleted. Give me a break.
Idea that 3 flags wouldautomagically delete garbage comments doesn't feel right either. It seems to be based on a shaky assumption that hundreds... thousands such comments would eventually collect enough eyeballs from users concerned enough to flag. Famous complaint about explosion of comments on Stack Overflow suggests that this way simply doesn't work.
