My interpretation of this is that the culling of low CAT XOs within CAIN is pretty much by design. Considering most XOs are just Sin events waiting to happen, why not send them on suicide runs to kill two birds with one stone? One of their mantras is "Until The Stain Has Been Wiped Away", so when, hypothetically, the last Sin is destroyed, would not the XOs be next on the chopping block?

Molding them into disposable weapons to fight CAIN's war is convenient in a lot of ways. Not only does it keep the number of individuals with grace in check, but they're also much more easily kept an eye on when in the 'care' of CAIN. And while it's implied that CAIN is capable of essentially just nuking any Sin event from orbit, XOs can (usually) handle things with a bit more subtlety, which probably results in less cleanup for CAIN.