Josh, see whether this is any help. There's a utlilty that you can use if you're having problems removing Java: How do I uninstall Java on my Windows machine? - 1.5.0, 6.0

Someone else had the same problem as you & it seemed to help them out. The thread's pretty old, but hopefully the advice is still good
Java Runtime Environment (JRE) - Unable to Uninstall JRE 5.0 update 4 - Already have this version installed