You are probably right. Or at least it will be much easier for the government to seize domains in the future. From what I have read in news reports, the legal justification that the onion sites were seized were dubious at best
It is already trivial for them to seize domains. It requires little more than them simply ordering the registrar to hand it over. Clearly, this is legally wrong and unconstitutional, since domains are a form of intangible property, but in actual practice, they're doing it on an almost daily basis.
(Seizing .onion pseudo-domains requires actually compromising the system, though.)
This has literally next to nothing to do with net neutrality, though.