If Ax kileld Visser two after landing the jet, it would be cold blooded murder. Not Ax's style. Besides, Visser Two's subordinates might have hunted them down if Ax killed the guy. Heck, if he's not going to kill Visser Three, what makes you think he'd hastily kill Visser Two? During the David Trilogy, I believe, Ax has Visser Three at his tail blade mid morph. He's got a good level of restraint.
I was thinking a little more like 'accidently pressing' a button, such as The Eject Button on the plane, to be honest. Make no mistake, writers opt for these things. Like it was done with Cassie, who 'accidently' fried that Hork-Bajir-Controller during The Unexpected.
Indeed, Ax truly has good restraint and he is no cold-blooded murderer, and I believe, he's also not a genocidal maniac, like he was almost forced to be during this stage with Visser Two.
The story goes to show that at this stage of the series, times had changed... And you have to ask yourself what you would have done...
I would not let this powerful enemy walk away unharmed so he could come back and bite me in the ass later...
And we weren't shown any subordinates to believe he had a massive crew of followers on Earth. As far as I know, Visser Two was portrayed doing a solo cameo.
And yeah, guys, we would have a lot less to discuss if the ending was more resolved. It's kinda cool imagining and coming up with all these things.