Huh, I thought I posted a 12 paragraph reply on this, but I don't see it. Short version: Starfleet probably has people that love Kirk AND people who hate him, and plenty in between. So it wouldn't be one mindset, it would be all these different views/opinions. Could be they HAD to give him a ship, but some worked it out so they gave him a turd of a ship.
The only way I can justify how paranoid Starfleet and Federation seem in SFS and TUC is that Sowards' original notion for TWOK - that SF has given up on 'to boldly go' in favor of just protecting its borders -- is something Bennett kept in mind even if he didn't make it a story point. And by TUC it was just an extension of that twist to make Kirk such a jerk.
I think NOT having that story point in TWOK was wrong, but only because the idea behind it was central to Kirk's problem - he had spent his career in service to an ideal being abandoned -- now that's a good basis for a mid-life crisis! It would also have set up the idea of going rogue later on, which is what I wish they'd done after SFS, because you wouldn't have had all the baggage and expense of showing Starfleet and spacedock and all that, and you could have concentrated on the characters living out their lives in a little ship doing important things (in retrospect, what I envisioned in 1984 probably isn't too far off from FIREFLY/SERENITY, only with better science.)
I guess I just really like some of these characters a lot more than the organization they serve, because too much is lip service to ideals, and the prime directive is a policy of mass murder.