Uh... hmm. . . I think it's observable behavior in game is much more like a cruiser don't you? I also don't know what you mean by "too well armed" since a Hyperion has both more anti-fighter and anti-cap ship firepower. Even disregarding table stats, the UEF deploys them like one would expect cruisers to be deployed.
Sanctus anti-capital firepower is much better than that of the Hyperion. Those two SBlues aren't that big an improvement over the Aeolus' SGreens (nearly twice as strong, but that's not saying much). The Sanctus has two mass drivers, two gauss cannons (each half as strong as the Karuna's), and two Warhammer torpedo launchers, and it'll kill a Hyperion in less than a minute with 80 - 60% health remaining. The pulse cannons deal most of the Hyperion's damage, but they don't help that much. Their fighter screens are roughly equivalent.
The Sanctus also has 67000hp, compared to the Deimos' 80000 and Hyperion's 40000 (and it has the corvette flag in the files, for whatever that's worth).
It's deployed the way it is simply because the Karuna fills the UEF's corvette role and lacks a proper cruiser. Like it says in the description, the Sanctus occupies a role between frigate and cruiser, and since frigates are basically heavy corvettes, I'd say that makes the Sanctus a light corvette. Its far superior combat performance when compared to actual cruisers supports this.
Agreed. Something named DESTROYER ought to be big and bad, I think.
Destroyers are called what they are in the real world because it was short for torpedo boat destroyer (as in, a ship that destroys torpedo boats), much like battleship was short for line-of-battle ship. Now they're both official designations in their own right.