The time in Termina could run different somehow than Hyrule. But since they're parallel worlds it's unlikely. What I mean is that when they are killed by link in the future, instead of dying like it seemed (why did they go to heaven anyway? ) maybe they were transported to Termina and the time there was when Link would've been a kid. So in MM it's actually at the time Ganondorf is sealed. Maybe they dont kill people cause their son is gone and they lost hope in taking over or the triforce affected them too and the sense of power left and they formed a potion business.

Just an idea