This could very well be true, but Kubrick also had ALOT of power and control over his films, so although it might have been a motive on his part, I doubt there was any pressure from studios, or if there were, that he gave it little thought.
Is there another couple or even unattached actors from the time you would have rather seen in the film?
I am actually a big fan of Cruise, as an actor, and think he was very good in this film. I think his public persona and his self as scientologist, and maybe even rumors around his sexual preferences, would give him a lot to draw from internally as he portrayed the role of someone dealing with so much inside while trying to carry off his persona as a successful doctor and family man. I guess most if not all people have this inner struggle to some degree, but I think Tom was a solid choice and was fantastic.
I also think the part where the frat/college type guys who call him homosexual slurs or whatever was a little on the nose when we consider how much interest is put into his sexual preferences. I'd be willing to bet this is one of the reasons Tom was picked, the amount of study that Kubrick puts into his films and casting is insane.
An often unpopular opinion I have is that Kidman actual gave the weaker of the two performances between them. Tom has a ton more to draw on than Kidman does with her character as a stay at home mom who used to work in the field she enjoys. Although as a woman, even with adopted children, maybe she felt this struggle to some degree, I just don't think the same way Tom may have with similarities to his character over the years. Maybe Tom does all the Mission Impossible stunts and other things to some degree to abate this idea, like Dr. Hartford goes out looking for sexual conquests to prove himself. The more I watch this film, the more I find that no one else could have done as well as Cruise did with the role, especially at the time.