Bases are always getting either targetted or hit and disabled.
So either have a guard the base option, defend the base option or have the option to have defenders
Guard The BaseHaving the option to use your ship as a blockade or some sort and have the legion who targetted the base disable you and/or the other members of the legion before continuing to attack the base.
Defend The BaseHaving a button to go to red alert or some sort of awareness to the base and other systems.
Have defendersHaving defenders say having a fighter bay on the base for base targets and launching fights out to engage the legion in question, etc. So its kind of like the idea of the thread
http://galaxylegion.com/forum/viewtopic.php?f=6&t=19543. And with every 100 ranks 5 fighters go and intercept the attack and draw it away from the base, etc