Total agreement with your entire post, but two things:
JJ Abrams also straddles this line.
The Enterprise appears bigger and tougher than the TOS and possibly even TMP Enterprise. There could well be a confidence throughout Starfleet that ships like her (and larger, I seem to recall that the saucer section debris she almost collided with over Vulcan was larger than she was) could handle anything they came across. In such an environment, the science argument could well hold sway, as they already feel they have their military bases covered.
The Abrams Enterprise is about the size of an Ambassador class, actually. The rest of Starfleet's ships are similarly large, which leads me to think that perhaps these larger-sized vessels were ALWAYS there and we simply never saw them until the TNG era. The smaller version of the Constitution class could easily still be in service out there somewhere, but post-Narada craziness meant both the name and the new ship contracts went to the larger vessels instead (say, they built eight of the smaller vessels instead of twelve to save room for two Enterprise-sized ships). The IDW comics imply this as well; Captain Robert April is said to have commanded an Enterprise that was decommissioned just a couple of years before Kirk's ship was built, a ship which in the Primeline would have been commanded by Christopher Pike and Number One.
The Narada owned them, but once again an anomaly, a one-off threat.
But Starfleet still defeated it, not with superior firepower, but by carefully analyzing its weaknesses and exploiting them. That seems to be Starfleet's primary advantage: a single starship isn't all that powerful, in fact Starfleet vessels tend not to be that impressive militarily. But they don't really have to be; they staff their ships with some of the most intelligent and innovative people in the galaxy, people who can devise fifteen different ways to kick you in the balls before you can lay a hand on them.
As with EVERY anomaly they encounter, the Narada is proof that Starfleet is the triumph of brains over brawn: they don't generally out-fight their enemies, they outsmart