"Chilling effect" has always been a profound term for me, because I imagine the "cold" (numbness really) sensation a human body often senses when something truly awful (disembowlment/dismemberment) occurs. The body's way of protecting itself is to go "cold", and in many ways that's exactly the effect taking place here, as well.
There's also an undeniable part of this conversation that rarely gets addressed simultaneously, and I'd like to see it sussed out more in concert; what about the folks who are doing Evil in these private channels? It's unacceptable to me that TOR gets used for child pornography, and it's unacceptable to me that my government finds out I'm gay before I come out to my family.
I don't want to provide those who would do Evil any safety or quarter. I also want to give people a powerful shield to protect themselves against judgement and persecution from the public and sometimes the law.
We should talk about achieving both of these goals, but we generally don't.
Evil is agnostic of location. Your question is of no significance. You might as well be perturbed over "Evil" people living in houses or eating food. Unsurprisingly, evil people are people and will tend towards the same activities people generally engage in.
We need to talk about how to create "no Evil/privacy", or at least how to approach something of that kind, even if an absolute version doesn't exist.
You have not established the slightest bit of an operational definition, and resort to pathologizing neutral transmission channels as hosts of "Evil". This is a complete non-starter and not worthwhile to deliberate. "Evil uses Tor" is as useful as "Evil uses paper".