eval string has a performance penalty, because the compiler has to do some work. However, since what you are about to eval first has to be fetched from disk, this doesn't matter - the disk I/O will dwarf the eval performance penalty.

Now, no doubt people will here will say you should avoid using string eval because of security concerns -- you're going to run "foreign code" -- aren't getting it. Since you're going to run modules dropped in by others, you're going to run "foreign code" anyway. After all, even a "use Module;" is mostly a big string eval anyway.

I'd say, if your current solution works for you - use it. As for your "should" questions, what you shouldn't do is ask on Perlmonks what your coding standards should be. Ask for the pro and cons of your alternatives, but don't let others decide what you should do. Remember that it's your job and responsibility - you are facing any consequences. Not the people here.