From: Vermont, USA
In analyzing how I've played this since being aware of the issue, I tend to do the following.
1. Steal the territory maps of other nearby pirate factions. Choose an independent world that is not one of the closer ones to their bases.
2. Position a resupply ship or build a mining base in the same system as that independent for quick and easy refueling.
3. Devote 4-5 ships, usually frigates or destroyers with both long and short range weapons, to (initially) raiding that independent and staying in its local space until I have 100% control.
4. Build the facility. Then keep those ships at the independent, just "move to" its gravity well and they'll float along with it.
5. Make sure the engagement stance for those ships means that they will attack anything hostile coming into the system. Do not have truces with pirate factions that are operating near that world.
6. I keep an eye on the system from the galaxy map while I do other things to make sure no unusual ship icons have showed up there. Whenever I get an alert that something is happening in that system, I pause and take a look. So I am micro-managing a bit, because sometimes the AI reacts a bit more slowly than I can and I want to make sure those ships are dealt with before they get to the planet.
7. If you have long range sensors, parking a base or ships with long range sensors there will also give you much more warning.
8. If you are playing a playstyle that takes longer to build facilities or has facilities costing more, this will be harder to accomplish.
I tried that again this morning and was able to complete a pirate base and fortress without interruption. In any case, we are already in the process of undoing the change that broke the base resiliency and we're taking the opportunity to make them a bit more interesting as well. Those fixes and improvements should be in the next update.