I agree that this certainly feels like it's a step back in terms of freedom for all users. Introducing these kind of measures and expecting them to be only used to punish morally wrong behavior is a form of exceptionalism. I don't think any institution can, in the long term, consistently have such moral insight and correctness.
Historically, I think those measures almost always ended up being abused at some point. Measuring whether they've been used to do more harm than good is where the question gets a lot more complicated.
However, I'd like to better understand why you believe that freedom is the main force of progress. Although I do feel like our society generally progresses towards more freedom, it isn't always the same kind of freedom that was present in the past.
For example, freedom surrounding gun rights, freedom from taxing or freedom from government interventionism in the economy (or what is perceived as such) have all, arguably, caused a lot of harm in the US. Do you feel these are all justified simply because they are "positive rights"?