That's incorrect.
Krelian actually shifted the WE at the end to prevent it from destroying the planet.
There was supposed to be a Xenogears sequel, after all.
But yeah, along the way, he did commit a few atrocities. In his mind, probably, the ends justifies the means.
I beg your pardon good sir, but the wave existence, freed from Deus, transcend our plane of existence and go back home, with Krelian in tow.
It never wanted to destroy anything.
And Krelian masterplan was hitching a ride. It involved working behind the scenes for centuries so the uber driver was at the right place at the right time, but that might be because they don't have uber dimensions in xenogears universe.
I guess squenix execs wanted a sequel, but let's not forget that the wave existence powered all the gears in the world through deus (an enabled the use of magic if i'm not mistaken). With deus destroyed and the wave existence gone, no more gears or magic. Try to do fun combat without those two.
Edit : What i meant in my first message is that Krelian doomed everything and everyone with his behind the scene shenanigans, not by freeing the wave existence.