''apple is not keen on java''
Really? V. surprised to hear that. Have you run Software Update? (off the Apple logo top left of your screen).
''How would I do this please''
The easiest way is to do an erase/clean install. Before you do anything though, back up all your important software, files, photos, music etc. then have a look at this:
http://support.apple.com/kb/HT3910?viewlocale=en_US
A bit overkill though imo if you're not Mac-savvy. I'd try and resolve your current Mountain Lion problems first.