Couldn't they just feed the really dangerous ones to 682?
They might make it stronger.
As the wiki comments often say: "Secure, Contain, Protect, not Destroy, Destroy, Destroy." Also some variation on "Don't cross the SCPs."
The way they terminate D-Class personnel at the end of each month seems kind of stupid and malicious on the Foundation's part. You'd think given the high turnover rate they wouldn't want to do away with whatever D-Class personnel they have left at the end of each month. The near sociopathy of the Foundation aside, it just seems incredibly wasteful.
Some of the writers either ignore that or claim that it's just propaganda used to keep the D-class in line. And then of course there are the others that treat the D-class like toilet paper.