It might not have been proven, just like they couldn't prove OJ killed his wife. He refused to give a DNA sample which would have cleared him immediately, had he been innocent. No one believed Basso was clean. When Discovery then goes and hires him afterwards, it really is the same as saying "on our team you can dope all you want".
And I agree that all teams who hire known dopers are making a mistake and sending a bad signal, but this one was exceptional. They obviously hired a dirty rider to win the tour for them, and didn't even care. I don't see how any discovery-rider can now have any credibility. I thought hiring Basso would have been suicide for Discovery. The other teams are at least giving the impression that they are trying to fight doping. Discovery are giving the impression that they don't care.
Now, I'm one of those people who doesn't really care who dopes (I think they all do it), but I would find it ridiculous if they pulled Rasmussen and gave the win to Contador.