My reading of the tea leaves says you're planning on rolling this app out onto a bunch of oddball departmental servers which are probably not under your direct control. If your school is anything like the university I worked at, that means some of those machines are crust old boxen that should just be shot and put out of their misery, but geology has to have that exact version of perl 4 to support their favorite app. Sigh.

So, what happens if the threaded code doesn't work on every single machine? Is the project a failure or will your PHBs be happy with 95% coverage? Can you go install a private version of perl on the machine in question? Is that ancient server lurking in some obscure corner of the campus going to come back to haunt you?

That said, sure, reasonably up to date versions of perl will typically be compiled with ithreads on the major platforms. Really, it's up to you to make the call, but those are the points I would consider.