[x] Stay at the Fortress and defend. This gives you the most time to prepare and the advantage of fixed defences. On the other hand, you have no idea how much concentration in force they can manage. You're basically betting that they will only throw five thousand tireless machines of War at you. Still that's likely a safe bet...assuming the war in the north is going well.
[X] Take your full army leavingonly a picket force behind and attack the approaching golems. This is audacious and could cost you the fortress you just spent a couple hundred lives taking. However, it gives you local superiority, and the ability to fight in detail, at least if it's not a trap.
[X] Split your forces, leave enough to match the force coming in but take half of your effective army and try to destroy the facility ahead of time. While this risks a lot, it does mean that you could potentially accomplish your mission and begin the long journey home soon. Still, six thousand against whatever is at the facility...