The solution is to prevent your system from being hacked. It would be better to spend your time auditing your system than on this.
while I can't prevent users to use the open source scripts (witch normally have a hole), then my best priority is to secure the server not the web sites, every one responsible on his hole but I can't allow to hack another users on the server.
Anyway, I guess cPanel had note this problem or security hole, and they now provide a new option in Apache builder, it's called Safe PHP CGI, and the description of it was : perevent users from overriding the system php.ini
But I think it's not stable yet, because it didn't work
I think it'll soon fixed, until that I'll pray to never lose the server if some hacker come by