"should the bad apples spoil the bunch?"

Absolutely!

If an organization is ruled by evil, there is no way that good would be allowed to thrive.

Real good isn't ignorant of their surroundings. fools are.

Real good knows when their organization is governed by evil.

Real good doesn't feel confortable in such situations and take actions, or leave to save their souls…

Those who remain loyal, even if apparently unconnected to evil actions are guilty by association.