Since Marianne also agreed to Charles's plan, why did V.V kill her? Was it just because he "thought" Charles will deviate from the plan because of his closeness to Marianne.
Actually it was just that V.V was jealous of her
In a flashback, it is revealed that V.V. was the one who assassinated Marianne, having done so out of jealousy. He lies about this to Charles, breaking his promise of mutual honesty between him and Charles.
but why was he jealous? probably because he thought that Charles was getting closer to Marianne and further away from him, enhanced by the fact they are twins and have that extra bond twins are thought to have
He is the older twin brother of Charles zi Britannia, but as he has become immortal at the early age of 10
Charles and V.V.'s childhood years were marred by an internal feud in the Imperial Family called the Emblem of Blood. This period filled with deception and assassination resulting in the deaths of various members of the royal court including their mother. This event convinced the two to create a Geass contract to create a world without lies and to do so, they intended to destroy the "Gods". Several years later, Marianne Vi Britannia and C.C. joined in their venture as well.
Source: V.V - Character Outline
As you can see from the quote above the two went through hell with the Emblem of Blood and created the contract between them to destroy Gods to create a world without lies. then years later Charles marries some commoner unlike Charles other wives and she joins in on their plans along with her Geass Contractor/Master.
Also after Marianne was killed Charles had her body taken away in the event she could be returned too it, sealed Anya's memories, made Nunnally blind and sent her and Lelouch to Japan to protect them. even though all of that came after the fact it does show that in a way Charles cares for Marianne and her children so V.V does have some ground in thinking his younger twin brother is being stolen by some woman.