I say add one or two fighter squadrons to fortress buildings. The planet then sends these out on a system-level. It won't make or break any fleet, but it will be a constant annoyance that WILL take back the system unless you deal with it. It's also a simple solution.
I think it makes sense and would be a great addition to a sci fi game.
I think that's the move. Uses an existing building, so you don't have to burn a whole building slot on one, relatively unusual situation, and having the fortress threaten control over the system really would force someone to engage with the ground-based forces.
I might even take it one step farther. Let the fortress add fighter squadrons as time goes on. Once it hits a certain number, it can send those squadrons to neighboring systems. That way your fortress world can actually threaten an entire footprint of space. (It would be even better if there were supply lines to disrupt, but threatening control of outposts is great too.)