The point of the 2A is exactly that, and the observation is true of any government in history. With sufficient power, there is little that stands in the way of gov't imposing its will absent the threat of any retaliation.
I do fail to see how this has ever been a "gov boot on a throat for collectivism", though. At no stage in our history has the gov't manufactured or been a real part in delivery of these vaccines - save for isolated incidents and it's stockpiles of certain things (anthrax, smallpox vaccines, etc.) and the gov't has never forcibly vaccinated anyone in quantities, nor will it ever, to my knowledge (outrageous isolated research being the exception) While people act like this is a 2A right's issue... what is your consequence for not vaccinating?
1) You can't have your child in public school, but you could in theory home school.
2) .... uh, nothing else.
Where's the gun owners going rabid about any Dick Tom and Steve being able to open carry in their kid's school? Anyone? Bueller?
So far the only record I've seen of anyone being penalized are in small epidemic areas subject to fine only.
What about speed limits, is that collectivism to not want people driving 95mph down residential streets? Bear in mind, speed limits are enforced more than any mandatory vaccine requirement - that would get you fined and arrested. If this threshold is the definition one has for collectivism, we're already the U.S.S.R.
Pathogens are invisible, and people fear needles / have ingrained borderline superstitions from culture. That's what the difference it outrage really boils down to. Can't see the risk, can see the pokey thing.