Missiles are dangerous as they will teamkill if you aren't carefull. Just make the stationturrets a lot stronger. Some pulse turrets on the bases, base turrets of different class: small turrets with a fighter-weapon-like punch (fast refire / speed / short range), medium turrets with a GB-turret-punch (medium refire / speed / range), heavy-sized turrets with a cruiser-turret-punch (slower refire / speed / good range).
Btw most turrets will be taken out by missiles from bigger ships...and if you want that to be used as a tactic, the bug where it doesn't show turrets / hull / etc in the targetscreen (lowerleftcorner) has to be fixed!