If the thing doesn't really work from on top of the tower, why is it there? Why don't they put a weapon that does the job on top of the tower? And what numbskull allowed a building that provides cover to be built within crossbow range of the tower? The whole point of a tower it to command territory around it, which it cannot do if the field of fire is cluttered with stuff.
This particular castle is a seat of government for a small city/baronetcy, designed more to impress and be useful for administering the city than for combat. The walls are only 20 ft. high, it has only 5 30 ft.-tall towers on the walls, and the gatehouse is just two of the towers with a heavy, iron-reinforced oak door between them.
Thinking of fortresses built for similar purposes, it's no Edinburgh Castle, but it's a better defense than say, Fort Nisqually.
Edinburgh Castle: http://www.edinburghcastle.gov.uk/
Fort Nisqually: http://www.metroparkstacoma.org/fort-publications
Anyhow, the ballista was doing well at shooting people on the open ground around the tower, and drove them back, but obviously the re-conquering troops took cover as best they could. It's held them off for about 10 rounds of plotting against it -- like a machinegun nest, it's pinning them down and making them reconsider an indirect approach. It's not a super weapon, but it's good.
I'm going with a 5-man crew and letting them aim at a new target and fire every round, with no to hit penalties. 1 man crew, every other round, and a big to hit penalty, as per the DMG rules (3.5e p. 99) doesn't make sense to me. It's a precision sniping weapon/light artillery, so it should have an artillery type crew, high accuracy, and a good rate of speed. Maybe 3 man crew, fire every other round, and no to hit penalty would actually be the most accurate way to run it, vis a vis history.
Any Roman artillery experts in the house?