Remember that one of the early ideas for Star Trek VI was that Saavik would have been revealed as the traitor aboard the Enterprise.
Roddenberry's reaction to that was that she was a beloved character and she wasn't to be tarnished.
Nick Meyer's reaction to Roddenberry's objection was that Meyer created Saavik, not Roddenberry, and when Roddenberry gave back any money he earned off of Saavik then Meyer might actually care what Roddenberry thought.
Roddenberry's objections to the film were very early in story and script stage. And Meyer walked out on a meeting with Roddenberry. Meyer didn't have to take Roddenberry's advice, and he didn't. At all.
Harve Bennett had tried to be polite to Roddenberry during his decade producing Star Trek movies, and Roddenberry did what he could to sabotage Bennett in the eyes of fandom. Meyer wasn't going to play that game, and if Roddenberry didn't like it, then so be it.
Saavik changed to Valeris because Kirstie Alley wasn't available or wasn't interested. It had nothing to do with Gene Roddenberry.
What Roddenberry thought of the finished version of Star Trek VI we'll never really know for certain.