My only concern about the Microsoft link is the fact that it’s so old. November of 2011. So I did a search in the Malware Protection site for “Java Rootkit” and got the following, sorted by date:
Looks bad. Every day another new one.
Still, as I said, we have several major apps we support that uses Java, and getting rid of them would be a sure PITA and a possible show stopper.
As a stopgap, ALWAYS ensure you antivirus/anti-spyware software is running always, and updated everyday!!!!!