Both of the situations you described can be accurate simultaneously.
There are two levels of civil government. The military can override the civil functions of the lower level (the states) while still taking orders from the upper level (the federal government)
In ordinary functioning of government and civil society there's an effective separation of the army and the police in law enforcement. In the US, this is governed by the posse comitatus act. Canada doesn't really have an analogue, the government can request the assistance of the army when lower levels of government are unable to perform their duties sufficiently to maintain order.
The use of the emergencies act makes it clear that this is one of those situations and allows the government to utilize the military to support lower levels of law enforcement.
This is not martial law. This is not a coup. This is not unprecedented - after all Pierre Trudeau used the War Measures Act (predecessor to the Emergencies Act) to restore order in the October Crisis.
This is more like a state calling in the national guard.
The answer to lower levels of government not being able to maintain order isn't to roll over. It's to bring in more help. That's what's being done here. And it's governed by the Charter. Much more stringently than the War Measures Act ever was.
[edit] We cannot allow a small, loud, group of individuals to overturn the democratic will of the people as decided in the last election. This is un-democratic, unfair, and must end immediately. We can talk about ending restrictions in the open, but not with a boot on our throats. This occupation must end before we decide on what to do next. I remind you of the interview Pierre Trudeau gave re: the October Crisis.
Pierre Trudeau: Yeah, well there's a lot of bleeding hearts around who just don't like to see people with helmets and guns. All I can say is, go on and bleed, but it's more important to keep law and order in this society than to be worried about weak-kneed people who don't like the looks of a soldier's helmet. [1]
I highly recommend listening to the longer speech [2]. Far more interesting than any speech given by Justin, IMO. Obviously a different situation, but with similar roots: wanting to overthrow a democratically elected government because they don't like the lawful, legal, constitutional decisions.
They can have their say in peaceful protest, in court or at the next election - and not before.
If it's unlawful, illegal or unconstitutional then avenues exist within the courts to resolve their grievances do they not? I'm led to believe that rule of law continues to prevail within Canada.
[edit] Not just that, Trudeau operates a minority government, meaning two other parties could gang up and oust them at basically any time. And yet, he remains in office. I think this really speaks to how small the vocal minority is.
They've brought guns, ammo, knives [1], built encampments, stashed them full of diesel and propane [2], disrupted trade, jobs, lives, supply chains, threatened violence. Harassed and intimidated healthcare workers. And for what? This is not your average picket, and it's gone on more than long enough.
We're all frustrated, we're all tired of this. I'm open to revisiting the health measures, but not like this.
There are two levels of civil government. The military can override the civil functions of the lower level (the states) while still taking orders from the upper level (the federal government)