For some reason, after destroying the turrets and conquering the stations, new turrets pop out of the station at 12.5% and on fire. Does that make sense? Given that they are brand new turrets at a station where they could rep for free, you'd think these new turrets would come out shiny and new.

It's been like that since... forever?

They do that so that it takes time for the station's defenses to build up and provides incentive for the newly-assigned owners to stick around and defend it because the weak turrets would be easy pickings for a re-capture. I'm pretty sure this was intentional.

Forever is a long time for something to be broken.

It is intentional as abortretryfail explained.

So you're rewarding the takers of the station with burnt turrets? Seems more like you're rewarding the losers for losing.

So at this point you just want the fire effects gone, right? ;)

Go get a repair module and fix up the turrets if you want them at 100% faster.