People mis-behave in caps... they'll do it in fighters.
You want to decrease the cap population?
How about you factions stop parading your caps around. That would cut down on quite a few.
How about you stop calling on those same indies you complain about whenever you get into a jam? Stop giving caps something to do and voila you'll quite a few more disappear.
How about getting your members to stop flying around in their indie caps? About a quarter the cap population drops then.
How about you report those so called problem ships or even try and explain to them what they are doing wrong? Try not barking orders and attempting to boss people around you'd be surprised how receptive people are.
How about factions utilize FR 2 and 5? Whoops there goes another couple caps.
I'm sure other people can think of more ways to potentially decrease capital ship numbers without granting official factions even more power over indies. But ALL other options should be exhausted (and the situation obsevred from the point of view of all the factions with caps) before granting official factions such power.
Cause lets be honest, an official faction with only six active members being able to decided what type of ship several dozen (or even hundreds) of players (of the same NPC faction) may pilot is laughable... at best.