I see you asking two questions:

1. Is Perl a sane pursuit for my career?
2. Should I stay with my company?

I can't answer your first question. I use Perl in my day job for convenient quick or large hacks, but as my boss doesn't learn Perl (he tried twice so far, and he knows enough other languages), our "main" programs are written in Python. The Python programs are the programs I write not only for my personal amusement but for the use by others.

Whether you really want to stay with a company that treats its employees the way you described is a completely different thing. Consider how most of the "valuable" senior programmers will behave - whether they will leave, or stay "until something better comes up", or stay and take a passive-aggressive stance, you'll have to live with the hostile work environment there. If all former Perl programmers will convert to Java programmers and everybody will live in lotus-eating happyness, that might be an option for you as well. My guess is that all Perl programmes will just be held within the company just until they've made themselves obsolete though, so I'd start looking.