Three does not seem to approve

That whole world is one bad day from a magic user collapsing an entire country if not more, so the usual "innocent until proven guilty" quickly becomes a very expensive luxury belief when applying it to magic users. I think that's the most important thing to remember when trying to judge the characters who have power in that universe: imagine you'd have ordinary humans walking around with all kinds of nuclear and biological weapons that could kill hundreds, if not thousands or hundred of thousands of people, potentially walking around at any time of the day. The paranoia around magic isn't unwarranted. Coming up with a good solution isn't easy.

I mean... the main element remains, this would give Nero or whomever actual indefinite control over said restricted weapons.

I don't fully grasp the intent, but I can see them, as previously stated, militarily match other forces. I can imagine them already having an anti-non-magic-user forces (like actual normal weapons) so that could round them up.
I guess GO's main weakness after overtaking Harrison was not having the MU protection other than specialized forces like the Palas.
I guess I do not yet know what Nero is pointing at, what MUs are a physical or political threat to him.

Sooooo yeah bad move Tobi, you build that controller then they take over the whole place making this tech and all its other weapons for the global order and probably not good things.