If more than a single Ballista needs to be manned, the penalty associated with such won't be a big concern. Even so, I'll eventually be large size.
I find the Ballista description suspicious given the fact that the DMG specifies it's just 1 round, and that it's treated as a large heavy crossbow.
In fact, look at the bottom left of page 103. It talks about asterisks, but I didn't see one in that area.
Page 65 in the Heroes of Battle supplement talks a bit about it too. It describes the system similar to what I got from the SRD though, and loading can be preformed all in 1 round according to it.
The justification for how they can all load, besides the Heroes of Battle book, goes into the process.
Let's say you are loading a catapult. You have a winching action, a latching action, and a putting the big rock on the bucket action,
Individual 1 starts his turn by turning the wench
Individual 2 starts his turn by grabbing the latch
Individual 3 starts his turn by grabbing a rock.
Individual 1 completes his move by getting the wench half way.
Individual 2 completes his move by applying the strain on the latch
Individual 3 completes his move by lifting the rock to waist height.
Individual 1 completes his standard by fully winching the thing down
Individual 2 completes his standard by fully connecting the latch to the proper setup
Individual 3 completes his standard by depositing the rock into the basket.
All of these actions require the winchman to be successful winching it down, but as long as the trust for success is there, it is just a matter of getting your job into the proper place on time. It's just like any other crew-served weapon.
A Youtube ExampleAlso, those who are interested in not having penalties from ballista, consider the ballista proficiency feat in Heroes of Battle.