Where assemblies and the like are vulnerable to being sabotaged and so on? Yes, I agree that's a big question. In Argentina in 2001 the assemblies were very powerful for a while, but apparently left political parties played some role in sapping the lief from them. All you can say is that people have to organise against this kind of political attack - which is where overt anarchist and libertarian socialist politics comes in.
For all their faults, the left parties won't be the enemy in such a period though. Argentina in 2001 isn't really a valid example, as revolution was never on the cards.
Anarchism and libertarianism don't exactly have a good record when it comes to withstanding attacks from either capitalists, the left or the right. Do they?