Microsoft has published a KB about disabling java in IE here: http://support.microsoft.com/kb/2751647
This is just a regkey so you could push it out to target machines via a custom action in protect. The process looks to be difficult to reverse so I'd read the entire article to ensure it's exactly what you want.
If you want to disable Java for firefox I believe it would be more complicated and may not be able to be done from Protect. There is a Sourceforge project named Firefox ADM which is a group policy template, and this would enable you to enforce this change across your organization.
Hopefully this was helpful, If you need assistance in configuring a custom action I suggest calling into the support desk as it's much easier to explain on the phone or a screen-sharing session.