It's because they've experienced first hand how batshit crazy working for the government is.The friends I have that may be the closest to identifying as sovereign citizens are all government employees or contractors.
Want to move your computer 10 feet to your new cubicle? You've got to call up someone, fill out forms, and schedule some time for maintenance personnel to do it for you. Then you need to do the same thing with the network folk, so your locked down computer can get on the network. Then you need to do the same thing with the telephone folks. All in all, it might take you a week to move offices.
And if you really don't believe things are this bad, just talk to any long time government employee. This red tape won't even make their top 10 head desk stories.
Now imagine you weren't moving 10 feet and the procedure makes sense.
Well, sure it's a bit Machiavellian but from what little I have gleaned it sounds like they were in a difficult position - leave and the world gets trashed. Stay and they get blamed for the inevitable invasion. Telling the humans to shove it they know best would be decried as being a bit too paternalistic which is an odd but pervasive sin in most Hollywoo cinema.
It's not great or even the least of the evils in front of them but it doesn't really turn the whole AUTOBOTS GOOD/DECEPTICONS BAD dynamic on its head.
Which'd been great had the US government not been written like incompetent idiots because Bay hates Obama.