Although the Federation built more ships (as it should, assuming they were expanding) were they better at fighting? The ending to TUC doesn't show the Excelsior to have more ability to kill a BOP than the Enterprise-A did. And as we've seen in the Dominion War ships like the Lakota in "Way of the Warrior" had to have her weapons upgraded to be competitive in the firepower department. So even though more ships were built and of the bigger variety, they were not necessarily built for combat without having to go back in for upgrades.
The evidence would agree with you, they werent at least at the time of TUC as they would likely have similar phaser banks (dependant on individual ship refits) and the same photon torpedoes. The only difference between the two in a tactical situation when it comes to weaponry would be the number of phaser banks, torpedo launchers and potentially the number of torpedoes carried. The other factor being the strength of the individual ships shields (both from a design point as well as power generation) and the strength of the spaceframe/hull during combat.
When it comes to the time of TUC I would say that Starfleet was deffinately more militaristic, a side affect of the post WOK Nick Meyer slant on the universe.
However I never believed Starfleet to be pure military, just more of one than during the TOS and TMP eras. To me Starfleet from TOS was an organisation tasked with exploration, scientific research as well as policing Federation borders, defense of Federation worlds and colonies and when needed war.
The military aspect of Starfleet is a question also asked by Scotty in STID when he asked "is that what we are now? I thought we were explorers?"
We cant consider the TNG/DS9/VOY era as it is so different to TOS as TOS is to the movie era.
Ships like the Enterprise, Excelsior and co were top line multi-role ships which could be tasked to be as comfortable surveying a planet as it would be to defend that planet from an agressor, something a ship like USS Grissom a pure science ship.
Getting back to TUC and 'mothballing the Starfleet' I think the general idea that this happened is due to the Enterprise being so quickly called in to be decomissioned and no other ships of her type being seen after. This was probably on the cards anyway with the Excelsior being seen as a larger and natural replacement to both the class and the Enterprise herself (as likely earned by her crew along with Excelsior's ensuring galactic peace).