But we were explicitly told that the fleets were hopping from one side of the UFP to the other during the war; this would not be consistent with ships of a certain design being stuck at a particular theater of war.
As for the "militia must be assimilated, resistance is futile" bit, the actual dialogue goes like this:
Admiral Whatley: "Now, Bajor's admission is only the beginning. Now comes the hard part. Federation council members have to be chosen, the Bajoran militia has to be absorbed into Starfleet. There are thousands of details that have to be overseen and you're our point man here. That means we need to depend on you more than ever."
Sisko: "Don't worry. I won't let you down."
The absorption appears to be inevitable, non-negotiable and total (as per the definite article), so what's actually left to debate is just the exact meaning of absorbing. Does it mean Bajorans will have to learn to say "Sir!" in English but can retain their uniforms, ranks and sidearms and do pretty much whatever they please outside UFP-wide crises? This is somewhat unlikely in face of the total lack of evidence for UFP "national" forces behaving like that. No matter what the color of your face or the number of your limbs, you wear Starfleet fashion and fly generic Starfleet ships. And unless you are human, you'll have to be very lucky to find even one compatriot to share the ship.
I agree with you
It is possible that Starfleet Command posts members of species that get along well on similar ships. Andorians and Vulcans may prefer operating on ships with crews that are predominantly of their own race, and as a result, we get more segregated postings for these species. However, this doesn't stop Starfleet command from posting these segregated ships anywhere in Federation territory. Just because there's a starfleet ship full of Vulcans doesn't mean it needs to be stationed near Vulcan.