Michael was worried about his territory. With the humans in war, losing it most of all, they will start doubting and stop believing. He will lose believers and I bet that’s important for him. When talking about the matter, they are never once talking about the safety of the humans but that he will lose followers and believers. Apperantly thats more important than the lives of the humans.
What we know about Michael and Metatron
Uriel says not many are allowed into heaven, yet Michael brought Metatron there. Now for what reason? What know is that he was a trusted friend who became the pet. When saying pet Metatron also makes a comment about how Uriel went through the same. Nothing actually pinpointing what it was but Uriel looks away, a sign of shame or that he hit the nail, while grasping the shoulder where the wing is missing. I assume being Michaels pet is kinda painful and Metatron probably took a few beatings as well once Michael wasn’t in the mood to be cute or found that Metatron had done something wrong.