I think the possibility that OP is worried about (making dissent illegal) is probably at least as radical as overturning the clause against ex post facto law (both would require Constitutional amendment AFAIK). So given the level of paranoia required to worry about the possibility that free speech will be gone in the US, the constitutional ban on ex post facto laws isn't really responsive.
I suspect it would be much, much easier to convince Americans to give up the ex post facto protections than the first amendment. This can simply be done by focusing anger at a series of high profile scummy but completely legal actions, and a proper amount of demagoguery against the "damn liberals and their ex post facto bullshit". Once that goes, the rest is easy to deal with.
This can simply be done by focusing anger at a series of high profile scummy but completely legal actions, and a proper amount of demagoguery against the "damn liberals and their ex post facto bullshit".
You could probably start with the MySpace bullying case. Add in some Wall Street bankers for good measure.
Further, retroactive punishment (in the form of harassment, being put on watch lists or no-fly lists, etc.) can still occur even in the absence of any specific ex post facto law.
Finally, with the retroactive extensions granted to copyright holders, the potential for this has already happened -- publishers have released new editions out-of-copyright works, only to find those works later placed back under copyright protection.
