i mean, my first reaction is "just play on".  not telling you your business, but having to conscript crews because of a strenuous war is kind of a cool historical detail, and the state of the ships is like a nice scar from a good fight.  moreover, since low grade crews improve much more rapidly, the actual liability involved going forward is pretty minimal.

but if details nag at you (i can relate) i believe you can SM damage and then SM repairs, get your grade up that way.  less "god mode" is scrap the ship and build new, its much faster and cheaper when you have the components in hand (unless you made the mistake of putting armor on the cursed thing...).  the RP for using industry to improve your crews?  i dunno, in the depths of the war your navy experimented with AI crew which were ultimately deemed insufficient.

avoid the problem recurring with more academies.  i have such a hard time getting a satisfactory suite of scientists that by the time i power my way through that problem with academies i have more crew than i can use, even with a high base grade

Crew grade only increases with damage, I think. But I think that you could make a bumerang build, refit your ships to a smaller hull, absorbing the fired crewmen to your crew pool and then refit them back the original ship. Cost time, money and material... But wait for your crew pool has increased with a lot more than you release, not sure how this will impact on your pool grade thou.