GCC and timers should be immediate and short term penalties, not long term time-sinks that cripple pilots from moving around for a quarter of an hour.
Allow pirate alliances to own systems just like the 4 militias can. Of course, you'll need to fix FW so that occupation means something but..
In Pirate systems gate guns either don't fire to the owning alliance, or just don't respond to GCCs. Other benefits could also apply.