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Then there's Janeway with her 1st officer being a former member of a literal terrorist organization along with a substantial fraction of her crew.
How is that any different from Sisko? His first officer and lots of his crew were former members of the Bajoran Resistance.
There might be a difference between a resistance to an occupier and a rebellion against your non-occupational government.
IIRC, a lot of the Maquis were Federation colonists whose worlds got handed over to the Cardassians due to a treaty they didn't get a say in. Is it really that different?
Yeah but the Marquis were just that, colonists. Bajor was the ancestral home to resistance fighters. I think that's why they're looked down upon a bit by the galaxy like yeah it sucks the planet you found outside of The Federation got traded off but you come from the largest galactic government, maybe choose a different rock?
I dont remember Sisko's crew getting recruited after trying and failing to overthrow him.