|Welcome to the Monastery|
I seem to remember ranting about something similar not too long ago. I still feel now, as I did then, that its basically down to the fact that virtually no-one will get sacked for recommending Java.
Plain and simple.
However, what companies will have to wake upto is the fact that implementing Java costs a lot more than they realise. It also takes, on average, a lot longer. So whilst in the short term things may look a little bleak, I wouldn't worry too much. Just treat this as an opportunity to keep your CV upto date :P.
From my own personal experience, where I work we have to do everything in ASP or Java. You have no idea how headbangly frustrating it is to have someone tell you you can't use Perl cos they installed a Matts Script and it got hacked. And then they want to replace it with one that you found 22 holes in (without trying).
However, on the plus side, some of my Perl tools are proving so useful that there's a secret underground forming of people needing, using and utilising Perl. Its been slow going but things are slowly coming around (much to save my sanity).
I realise this may not help you, as your company is moving away from Perl but I think it at least indicates thats there's life in the old dog yet.
Of course once you have all that web development experience in Java, you can say ta very much and then get a new job. I would :).