You are right, if you choose the light side then the planet is destroyed and if you choose dark side then the planet stays intact.
My solution is that when the planet blew up as shown in the game the planet simply broken into large pieces. Remember in Star Wars episode 4, Alderaan was blown into pieces and the result is a cluster of rocks from the former planet.
When you fly to the planet, you only land on part of what is left of Malachor V. This piece of the planet will contain part of the old Sith Academy from kotor2.
The intro fly scene for MalachorV, light side, the Ebon Hawk will be flying though some asteroids or the cut scene of it flying through the storm of MalachorV which are already in kotor2.
The intro fly scene for MalachorV, dark side, will be the same as in kotor2 when the Exile goes to the planet.
Malachor V will be small but the purpose of the planet is important to the story.
Things you will see on MalachorV will be force beasts,.. Disciples of Kreia,… the Spirit of Kreia herself….and …..
MORE TO COME…….