It really comes down to the "villain won't kill the hero when he has the chance so he can design an unnecessarily complex and elaborate death" cliche, although for a straight to video Disney sequel it's actually a lot more well thought out than you might expect. Jafar didn't just want to kill Aladdin he wanted to disgrace his name so that Aladdin would die a traitor instead of a hero which is why he let him live long enough to be framed for the Sultan's murder. On top of that he revealed himself just before Aladdin was to be executed so that Aladdin would die knowing that Jafar had beaten him. Basically Jafar wanted to kill Aladdin when he was at his weakest so that he would die a far more psychologically painful death.