I don't know about this... I don't remember the game treating the pregnancy ending like it was a death sentence. It would have been a lot sadder. IIRC it was portrayed as bittersweet and not a tragedy. Don't you think MC would have made a bigger deal about it? "I killed my sister because I couldn't control my impulses" or something.
The ending is just shown to be loving, you don't see past the pregnant shots of her.
But surely you can understand if a jug of water has a hole in the bottom of it that it'll empty itself whether you're watching it or not.
She has a condition that is going to kill her because she's too weak. If you make her orgasm too much in one night you will kill her, before the completion of the grand adventure and the life essence transferal. If instead of going on the adventure to save her life you make someone that weak host a parasite instead what do you think is going to happen?
The series has done a fake pregnancy fakeout and continued past the credits, it's not a foreign concept to them. You don't get the option to continue the adventure after the baby, that implies it's too late to have one. Since the other ending gets a whole DLC and hints to a franchise, that one is going to be the canonical ending.
I'm sure Inusuku hasn't thought too deeply about the whole pregnancy ending leading to Imouto's death, but they haven't left any room for anything else to happen. If she doesn't die in childbirth, it's likely to leave her so weak that it'd be too late for the life transferal to do anything. Imouto would never be able to reach the witch in any case.