You wouldn't have necessarily been under Enclave control, the Enclave would be expecting you all to follow orders but should you and other dwellers chose to not then manpower would be on your side, though unless things went really lucky the Vault would take some nasty casualties cause it turns out men in advanced, experimental power armor are an utter bitch to take down and are pretty good at cutting through enemy combatants. That being said I can fully understand that sort of a scenario/premise being unappealing to someone.
And true, you wouldn't necessarily have to go back to the Enclave, they'd just expect you to. Since you'd have at least one SSBN by then you'd be able to go around and see how shitty things look elsewhere in the globe and just dick around in your submarine, see if any other nation's navies have survived and are floating around or beached anywhere, maybe shoot a whale with a torpedo for fun, idk.