I'm inclined to agree with Zien, and if people are just sensible about how they use Checkpoints, there's no reason for it to ruin exam prep.
By sensible, I mean perhaps not touching questions from before like 2008. In physics, for example, the VCAA questions go back to like 1993 on occasion - are you honestly going to be doing exams from then? The Checkpoints for Chemistry and Physics, at the least, have a stack of either very old questions or completely new questions, both of which shouldn't affect doing practice exams.
Basically, there's still a *lot* to get out of Checkpoints even if you avoid the questions that might affect exam preparation - they're still well worth it, in my opinion.