The way I maybe head cannoned it, Irenicus was trying to concentrate the Bhaal-essence into himself, giving Bodhi Imoen's soul but taking the god essence he needed for his grand scheme. Of course Imoen's essence level was lesser than the MC...for reasons, the PC's Bhaal-rating was of course over 9000.
It's also true that removing the soul still left trace amounts of Bhaal's essence behind, we become the Slayer during this period, which I still figured would be enough to spread around to Sarevok.