Hmm, I wasn't aware of the morph-capable Yeerk theory, even so I'm surprised the Yeerk in Jake's head, for all his alleged intellect was so determined not to ruin his host that taking him down with him or at least threatening to, never occured to him. Maybe he thought he'd be rescued even to the end, maybe he just figured the Animorphs wouldn't be swayed by such a threat since no Yeerk would.
Or maybe he was just so scared, alone and afraid. Maybe he didn't wish Jake any ill will since he was dying. Maybe in the end we're not so different after all . . . all just frightened little creatures who want nothing more or less than our freedom and prosperity even at the expense of others and--HAH, you're a fly forever now Jake, take that! You won't be a thorn in Visser Three's side anymore!