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.
Blocking a domain does not block a P2P application such as Bitcoin.
It has everything to do with this proposed plan to regulate the internet as a utility, because as you admitted that in order to actually enforce it they need to be able to identify at the protocol layer, which means they can then technically block stuff like Bitcoin and more specifically they can technically put actual content filters on the internet to block certain speech.
The reason they are attempting to implement this now, is because they want to be able to control what the public can see as they ramp up the GLOBAL POLICE STATE to
Orwellian ideals (think Obama's czars).
Ministry of Peace
The Ministry of Peace supports Oceania's perpetual war.
Ministry of Plenty
The Ministry of Plenty rations and controls food, goods, and domestic production; every fiscal quarter, the Miniplenty publishes false claims of having raised the standard of living, when it has, in fact, reduced rations, availability, and production. The Minitrue substantiates the Miniplenty claims by revising historical records to report numbers supporting the current, "increased rations".
Ministry of Truth
The Ministry of Truth controls information: news, entertainment, education, and the arts. Winston Smith works in the Minitrue RecDep (Records Department), "rectifying" historical records to concord with Big Brother's current pronouncements, thus everything the Party says is true.
Ministry of Love
The Ministry of Love identifies, monitors, arrests, and converts real and imagined dissidents. In Winston's experience, the dissident is beaten and tortured, then, when near-broken, is sent to Room 101 to face "the worst thing in the world" — until love for Big Brother and the Party replaces dissension.
You aren't the sharpest tool in the shed.