I like Jinx's ideas... I think it would be very balanced and add a realism to things in regards to capital ships. Right now the only way a player is really going to have high costs on a BS is if someone intentionally targets their hardpoints or they go weeks without repairing anything.
I like the idea of the shield mount being on the outside of the ship so it can be destroyed when the shields are dropped. Very very good idea. Would definately increase maintenance cost having shields targetable.
On a side note, these are some traits (however unrelated to getting the population down) that I think would be nice and rather realistic for cap ships:
All Cap Ship Weapons require projectile/power cell ammunition.
Cap Ship Ammo Prices about $500 credits per shot. (10k shots = 5mil)
Cap Ship Ammo hold roughly 10,000 shots per ammo type (Modifiable through ammo "size" type value, which is doable, I've done it before)
Cap Ship Weapon Power Increased
Cap Ship Projectile Weapons have 5k range
Cap Ship Energy Weapons have 3k Range
Repair Costs Raised
Shields about 20k power, with 500-ish regen.
Shields mounted externally
Armor upgraded drastically
EDIT:
Just a side note on the ammunition, 5 Million Credits would buy 10k shots of ammo. Now assuming that each one of your guns has a seperate ammo type you could fire for 5,000 seconds. Now if you say have all 12 of the same turret you can only fire for 416 Seconds, which is just under 7 minutes of constant fire. What this would do is give capital ships an "effective lifespan" in battle before they would be required to either retreat, or have a support ship (such as a repair ship) come in with a new load of ammunition.
That would effectively make capital ships only a realistic investment for factions with the ability to support them, making it VERY unrealistic for a independent capital ship to wander around, especially PVP-Whoring.
EDIT2: Oh, and ammo requirements would help prevent suicide repairs, cuz when you die.. your ammo is floating in space waiting for anyone who wants it to snag it and make a quick buck!