So the problem here is one of framing. Without the polemic slant, here's what you've effectively said:
Gun control.
Cost: lessens ability of one societal subgroup to wage a violent revolution, the possibility of which puts a check on society at large, when that subgroup's grievances are legitimate.
Benefit: lessens ability of one societal subgroup to wage a violent revolution, the possibility of which puts a check on society at large, when that subgroup's grievances aren't legitimate.
Strong encryption (and other anonymizing technologies).
Benefit: lessens society's ability to curtail the activities of people the society doesn't like (who just happen to have different points of view).
Cost: lessens society's ability to curtail the activities of people the society doesn't like (from people that are actually bad).
See, the thing about both of these things (from the point of view of an individual) is that they both form direct checks against society.
In the case of encryption+anonymity, society can't know who to target, and in the case of firearms law, society will think twice about attacking others physically.
So you're not going to need to deal with, say, parts of society that actually have the power to get you fired because you have a political opinion that contradicts theirs- maybe it's something completely ridiculous (like you're an actual 1945 Nazi), or maybe it's something more subtle (maybe you're Brendan Eich or James Damore). Or maybe you're an environmental or civil rights leader with some dirty laundry that would hurt you if aired.
And reality bears this out. Ever wonder why Germans are highly protective of their privacy? The Stasi, that's why- the dominant group in the geographical area of East Germany wreaked absolute havoc because society trusted them to do the right thing (just like they trusted the Nazis).
Ever wonder why the Czechs are highly protective of their firearms?
Same deal- their people could not advance and prosper because a certain other nation kept killing them (also the secret police thing).
These people know the evil that society does when it runs amok, and know why it can't be trusted with these tools.
They favor strong protections that individuals can use to escape society's fickle desires (like banning whatever boogeyman's in the news this week).
And society is notoriously bad at determining good from the bad and right from wrong; when it gets it really wrong, lots of people die.
Germany, China, USSR; all societies that have very little in the way of stopping the majority from abusing its power, and all who have killed tens of millions of their own people.
Now sure, individuals in a given society may vary in how comfortable they are with trusting said society (there are some good things that can come of it; environmental regulations and affordable healthcare being two notable examples)- but to say that there are some liberties that are fundamentally incomparable is disingenuous.
Unless the society you trust tells you otherwise, of course.