What weapon did you use to kill him with on the Desert level? I think the only weapons you can get with Qui-Gon on both previous Desert levels are a single blaster rifle and some flash grenades...and I think a Thermal Detonator is possible somewhere. Regardless, he's supposed to be able to deflect blaster shots away, and I thought that was working rather well.
It sounds like you definitely found a bug in Maul's AI in Assault that would make him killable. You achieved something that LA's Testing Department didn't
And, by the way, that's not Maul groaning at the end of the Final Battle level, it was Qui-Gon. I know, it looks like it - we were originally having Maul fall down the pit like in the movie, but something BAD was happening with the AI that made it not work, so we were forced to keep him dead on the catwalk