I hear you mentioned it was a repair dock for medium ships, but I was wondering - it may even sound obvious - but it would be a great platform for fighter/bomber fast repair and resupply. It's like having the good old 5T truck on your back refreshing and resupplying the troops on the fly.
I realize this is an engineering vessel, not a war machine, but if you were to equip some defensive armament, might I suggest a mass driver? You could run it the length of the vessel, allowing it to accelerate projectiles to enormous speeds (you could probably even use the tractor beam to do it, if specially applied). The only problem with this scheme is that the ship could only hit something directly in front of it, which might call for some maneuverable steering or additional weapons (of course, this isn't a warship, so one weapon might be enough in this case).
One of the conditions was the complete lack of weapons. An engineering barge, it can be and the repair dock for medium ships and a platform to build stations.