Skuzzy - Dred is right. If you are rendering JS at all under IE without a Sun JRE installed, you're using the MSJVM, which has been out of support status for going on 3 years now. In short, you're taking the risk that the older,now slightly more obscure Microsoft Java Engine that's currently unsupported won't be exploited. (Assuming it hasn't already).
Since EVERY Windows system up until 2007 had it installed, it's a pretty big target - that's a bet I wouldn't take.
Do a backup, image your disk as a precaution, make a system restore point, install the newest Java. I don't know of anyone else who had the same experience that you did - it's most likely that something else you'd ran previously set you up for the crash. (I know, I know, that never ever happens with Microsoft software....)
A little paranoia is a good thing - but remember, too much just makes you paranoid. {grin}
<S>