You can’t take over the US with 5 guys.

Well... if one of them has super psychic powers and another can pick up a tank and hit you with it... Its also worth taking a step back and recognizing John Locke's theory of Consent of the Governed does not hold up particularly well in the DC Universe. Powerful Metas are taking over small nations left and right.

The government has nukes.

Okay, sure. But every time you use a nuke, you get five new radioactive themed supers. So you gotta use those judiciously.

Had Batman done nothing the coup would have failed and the serum would have been forgotten.

That's a huge leap. Had he done nothing, the coup would have forced Star Labs or the Suicide Squad or some equivalent to intervene. And then you'd just get a different group of Meta-humans dabbling with super-drugs. And besides, its not like Magic Steroids are a hard sell in a setting where half the new wave crime bosses are trying to get into fist fights with Superman.

he sees that Batman is the single point of failure

To that end, I'd argue Batman's Babel Protocols as a bigger issue than Bane fixating on Gotham. Less that Batman is a single point of failure than that he's written as this Ubermensch who needs to outclass all the other Metas in the Justice League.

He's a singular point of overwhelming strength that only really exists as a counterpoint to the high fantasy impossible people surrounding him. And then, as a consequence of him being on such a high level, all his enemies also have to be able to feasibly beat up Superman our outpace The Flash.

This gets you to Joke functioning as a literal demi-god.

And that's not really a "Batman" problem but a "Writers getting into a dick-swinging competition" problem.