Well, at work, our main production servers run the front end of our databases in java and will for the foreseeable future, 3rd party application, no internet access for these guys. IT wants our shared machines to exclusively use IE because they can then track 100% of the browser activity for HR, these are the machines that our production personnel exclusively use to make my company money so I can buy expensive surface pros.also Java is being phased out completely and HTML5 is the replacement... so why would you want to install/have Java? :
As for the infection, hopefully the op can get up a couple screenshots so that this can get resolved. Infection in the RT environment would suck.