I just released Template-AutoFilter
to CPAN, which means it'll be available for installation in a few hours. It solves the problem cleanly by sub-classing Template::Toolkit with a modified parser that adds filter instructions to unfiltered tokens and supplying a pass-through filter for exclusion.
I've only done very restricted testing on it, so please do poke me if it breaks things for you, but aside from that it should not be very dangerous to use as long as you remember that it tries to filter ALL TT instructions.
If you're the impatient type, you can get the code from Github
as well. :)