I never thought Simba's overprotectiveness had been a problem, except for Kiara's hunt lol. I think that Simba had a reason to be paranoid, there's a whole pride out for his blood and that could put anyone on edge, King or not. I mean, Zira's crazy schizoid self was very vocal about wanting revenge.
Life is a series of interruptions interrupted by interruptions and I am the best kind of interruption.
But at the same time, you have to ask why, if Zira was so determined to kill him and he knew it, that he didn't finish her off the moment she set paw into the Pride Lands?
It could be that Simba's over-protectiveness is a matter of him not knowing what to do in relations of Zira. Mufasa's teachings tell him not to kill her, but at the same time, keeping her alive is a huge risk that is a gamble with other's lives - specifically Kiara.
I agree, it's kind of stupid for Simba to have her still around instead of ending her when he had the chance. I think it's actually consistent with his character, he didn't kill Scar and gave him a chance to run away during their battle. I'm wouldn't be too surprised if he did the same thing with Zira.
Life is a series of interruptions interrupted by interruptions and I am the best kind of interruption.