#KK,
No problem, I can understand how many pm's you must get,
So I sent you another.
Anyway here's my progress report, just to prove I'm not insane... I hope you don't mind that I post this here Bwian...
Siege engines replaced with a boulders, well an untexured cannon ball from the unit_models/equipment_library (I think any mesh would do...)
This also includes all crew loading and firing anims changed for Javelin throwing anims, however the crew only shuffle back and forwards as the 'engine' fires. All the engine anims are set to idle...
End result.
Not brilliant, but for an hours work and only 1 CTD on the way its my kind of progress...
With the crew anims adressed properly this should be a half decent workaround. 
#Edit
Ok a little later and here is a refined version.
In the battle_models.db I changed the AS trebuchet crew anim from M2TW_trebuschet to M2TW_fast_javelin and got a proper throwing action, albeit 1 handed. Although there is still some 'pushing' animation.
A few minor problems;
1) The engine anims need to be left as in the original or you lose the ability to target walls, no real problem there. The Cannon balls remain static anyway.
2) Not everyone fires.
3) Some crewmen die when they throw their own rock, probably a missile_poss problem, that can hopefully be ironed out.
4) In custom battle at least, you still need some 'built' siege equipment.
5) That 'pushing' animation, almost ruins the effect.
I understand that it is possible to edit a mesh so that in game it is invisible? That would be better than seeing the cannon ball. Or I guess a 'dot' sized mesh could be used instead.
In conclusion, with some more testing and refinement, this should work very well. With some giant sized, 2 handed throwing anims created, this should work perfectly. 
Does anyone know what the following refers to in descr_engines
sa_range 50.0
sa_friendly_range 75.0