Winner, I don't think anyone is bothered by the idea of going after the worst offenders - leaders of the regime, those who put the policies in place and those who carried them out, ie, the secret police themselves. But the big problem with going after the bulk of the informants, even if the vast majority were as opportunistic as you say - and I tend to doubt that, I would imagine that more people informed out of fear than you are letting on - is a logistical nightmare.
It's simply not possible to punish that many people, and even if it were, I imagine that most of the worst offenders were probably never kept on any sort of filing system. What's the point of having secret informants, if you put their name in four different files, and triplicate the lot of them? And for that matter, I sincerely doubt that 5% of the population, or whatever it was in Czechia, is just going to lay down and let themselves be sent to prison or forced labour camps. Even the hint that harsh punishment is coming their way will cause a mass exodus, riots, or likely both. And that's leaving aside the legal considerations completely.
I agree with Arwon's suggestion of a Truth and Rconciliation Commission, a la South Africa. It may not be pretty, but amnesty to all but the absolute worst offenders is about the best that can be achieved, and it's far better to admit the wrongdoings of the past and mose on, than to launch a mad crusade of vengeance against the wrongdoers. Do that, and you're likely to fall right back into some other form of "-ism."