While there might have been a general amnesty after the Dominion War, it make no sense that Ro would remain in Starfleet in any capacity. And if she went into the Bajorian Militia, Starfleet would not want her on DS9 and would strongly request her not to be assigned there.
She simply couldn't be trusted.
Which is exactly what happened, in the books. Except, Colonel Kira, DS9's commander at the time, saw something of herself in Ro. And Captain Picard personally vouched for her. And since Bajor wasn't yet a Federation member they could post their Militia members anywhere they want, including DS9, regardless if Starfleet wanted her there or not (which they didn't). Once Bajor joined the federation and the Bajorian Militia was absorbed into Starfleet then there was an issue with Ro staying, but... spoilers...