It was been quite some time since I have seen this episode, all I remember was that neither side trusted the other.
I see little human in working with and for the Founders, the Borg of the Gamma Quadrant. Call me simple-minded, but for me theocracy is fascism and fascism is obviously evil. Our human pedophile-protector and women-beheading theocracies (Vatican and Iran) are already quite disgusting, a fictional institution (together with all its minions !!!) which wants to conquer the whole galaxy and subjugate all humanoid lifeforms is plain evil.
Still worshipping your gods while not being that nasty to your enemies might be cute on a personal level but it doesn't make you any less evil on a political evil. You first gotta kill your gods, your Popes, your Zars, your Mullahs, your Founders.