Actually, it makes perfect sense.
1)Mutants are a valuable source of power (basically free super humans if you can force them to work for you).
2)letting them join Krakoa just makes it more powerful, and if you view it as a potential threat, then you don't want that to happen.
I'll simplify it for you.
All resources are scarce, all human desires are infinite.
As such, making sure MY group has enough takes priority, and if that comes at the expense of OTHER groups, so be it - after all, they think the same of me.
There - human conflict explained at its most basic.