TG, I gather from your comment that a single function in kses.php is used to strip scripts both out of posts and out of comments. Correct?
Is there a way to apply that filter only to comments but not posts? I think this would solve the problem, as well as the related problem of including php code in a post, which has been discussed on this forum before.
If there is currently no way to do this I'd like to make it a feature request. Or if posts rely on kses.php in some way (to make Quicktags work?), I would advocate having 2 separate functions, kses-posts.php and kses-comments.php or something along those lines.