Actually, I've managed to completely wipe out all Unity soldiers and decommission all security equipment at some large bases...however, it's not quick and easy. It requires nearly infinite patience, tortuous stealth, and a great deal of time.
The first objective is to penetrate the desired base without detection (parking a Unity vehicle at an automatic gate works wonders, but there are always one or two holes in their "secure" perimeters you may exploit with great stealth). You'll be using a lot of mark-and-execute maneuvers in combinations with a lot of retreat and relocate tactics; Unity soldiers will "sense" from which direction (bearing) those offensive orders were issued from, so you'll need to retreat and move laterally away from the enemies' target area, using more mark-and-execute as cooldown permits.
With the primary objective in mind, you can usually take out all alarm towers to prevent incoming defensive air support (secondary objective), sniping at them long-distance. You usually cannot take out the power generators this way, but only sometimes.
The tertiary objective is to locate and neutralize the power generators. Then, free prisoners to create chaos, but don't intervene to save them; call in rebel support, but leave them to their devices.
After that, press forward alternating mark-and-execute with long-distance sniping to engage the enemy. Plan on doing a lot of retreating, "strategic withdrawals." I've actually managed to secure some large bases without direct engagement (sighted by enemy), with zero revivals. It can be done, but it may require over an hour of actual gameplay. Try a more direct and less stealthy approach, and you'll trigger a level four Unity alert...which will require running a LONG way away without detection. Return and pick off the survivors (thank God the soldiers don't respawn!). The higher the territory's difficulty level, the longer it's going to take, and the more stealth that shall be required.
There IS no quick and dirty method of doing this.
There is a Unidad compound in Monte Puchu with literally zero guards and a handful of vehicles. The downside is it's literally at the edge of the map (at -13.0434, -609135) - it's at the end of the train line.
I actually spoke about this in another topic back in June, but a Unidad base with zero troops would be ideal as a "staging area". Sadly there's no helipad.