1)
Why did he say "you and your sons will be with me"?
1.
Rashi citing Brachos 12b: You will be in my place [in the world to come]. 1
2.
Radak: You will be dead, like me.
2)
Why will Yisrael be handed over to the Pelishtim?
1.
Malbim: They also were part of the sin [of not totally destroying Amalek]. They had mercy on the animals. They should have protested against Sha'ul, since they knew the Navi's command!