Normally, the AI will shoot it as the rocket belongs to team "mutant" which is allied/gdi and soviet/nod's common enemy. It was set up as mutant because you can't change the rocket's team after the team of the player that launched it (so that enemy AA will shoot it).
If I would've let it as team soviet, the problem would've been : "What happens if an allied soldier hijacks an V3 Launcher Truck ?" . Since the V3's team would've been soviet, if that missile would've been launched to the soviet base, then : 1. the AI would recognize it as its teammate and not shoot it. 2.if FF is OFF then it wouldn't have damaged nothing!
Thus, I've set the V3's team as Mutant so that regardless of who launches it, whatever the missile will hit, will be damaged/destroyed/killed and attacked by AA defenses.
The only issue here is that the rocket being Mutant, if you launch the V3 from your base, your AA will try to shoot it down, so you'll have to make sure that the rocket's path won't cross over your base.
Also, due to detonation timing issues, you wouldn't be able to launch the V3 on short trajectories and you'll also have a very small vertical tilt, allowing you to fire only at long trajectories.