As Poe said above, MM takes place in a parallel universe (also stated in the MM game manual) and as such, things that happen in one world do not necessarily effect the other, or happen in the other. This includes what happens to people in one vs. the other, and how people act in one vs. the other.
Twinrova did indeed die in OoT, however their parallel counterpart in MM lives in another 'universe' or 'dimension'. A world that shares some similarities to Hyrule, but is in fact a different world entirely. The death of Twinrova in Hyrule thus has no effect on the Koume and Kotake of Termina, because the Koume and Kotake of Termina are separate beings from the Twinrova of OoT.
As separate beings, their personalities are different than the OoT Twinrova as well. This would explain the 'Evil' Koume and Kotake of OoT and the 'Good' Koume and Kotake of MM. Because they are actually different people, in different universes, they are different, even though they are also the same.