IE 6 does not allow for plugins. So there you need Active-X control.
So all in all, regarding the servr side let perl do the stuff, or let it cooperate with the java you already have.
There is NO NEED to replace a working solution if its not buggy. But for the client side, why don't you just use java?
C'mon man, it's a standard :-) Do you really want to reinvent the wheel by reimplementing a full blown java application into perl? Yes, I had a look at your previous posts ;-)
Well, interesting it will become in the future anyway, when your java runs on anything but not on Windows XP. But there ActivePerl will run and allow for perlscript, but sadly, wich "normal" webuser wants to install that huge package just to use your site?

Have a nice day
All decision is left to your taste