I think you can pretty much kill anything if you heat your spacecraft enough. Of course, you might kill the spacecraft too. It might be very difficult indeed to destroy certain types of spores, and the "cook the spacecraft until they're all dead" approach might be possible but completely impractical for any real budget. Obviously any temperature that's hot enough to melt standard space-hardened circuit boards is going to be difficult. On the other hand, it sounds like the clean room approach is no panacea either.

As an interesting tangent, the engineering used to design a heat-resistant spacecraft might be re-used to design a long-lived Venus surface probe.