Sisko sort of lost his virginity on that one since a few months later he simply asks Worf to kill Gowron.
Sisko had a moral responsibility, as a leader in a time of war, to keep his allies from sabotaging their opportunities for victory. He wasn't sanctioning Gowron's murder, he was suggesting that the time had come for a Klingon reshuffling of power. It's not his fault that the Klingon recourse for everything is a fight to the death.