One thing I do when I have an unprotected system is I pick the tactical surrender option to avoid a massacure of my civilians, but something in the fluff makes me thing about something.  It says a tactical surrender makes the system easier to take back.  How about that's because hold outs are biding their time until help can arrive?  If you picked tactical surrender (or maybe researched some kind of covert communications technology) when you are taking back a planet you lost (or has a massive disaproval rate with its rulers) you can pick the option Coordinate With Resistance when taking the planet, which has a chance to disable defensive improvements and reinforce your army, with the local population being more likely to suffer losses as a result.