F/Z

Even if Kayneth couldn't contact Lancer due to his fried magic circuits, he could have used his command seal to do it. Those are seperate from the mage's own magic, as shown during the fight between Kiritsugu and Kirei.
I also don't believe Kayneth was glad to get rid of Lancer. If he wanted to get rid of him, he could have just ordered him to do something suicidal, like "kill Archer and his master" or some such thing. He also seemed to revel in being able to torment Lancer as his master and looked completely dead inside as he watched Lancer kill himself.

If we assume that blowing up the plane would be guaranteed to destroy everything contageous on it, then that means Kiritsugu had even less of a reason to not let Natalia attempt some kind of emergency landing and escape before blowing it up, or at least just let her jump out and try her luck. I understand his character just fine, but I can't find any reason for him not to give Natalia some kind of head's up and escape option before blowing up the plane. There would be no risk.