I think there is absolutely no chance the show ends like that - it is clear that this is set up to provide a show that does not rely on Starfleet and to give a different perspective.
If I were in charge I'd have the end bring in a hopeful scene, like Jean-Luc looking at Starfleet Command where things have been going down that indicate that everything just might be okay again - but he himself won't be involved in it. However, he can still walk away (maybe with his doggo pal Number One beside him) with a smile because he knows the next generation (ba-dum-tssssh) will see to it that things go back to the way they should be.