While it’s true that Raj won’t be as overtly difficult as Sheldon was, his presence will likely take some of the focus away from whatever issues Penny and Leonard need to deal with.
And, obviously, this will only mean that their problems will be ignored and might fester, as opposed to them actually getting better.
If you think about it, Beverly might have a pretty good point.
But, now that he’s not an issue anymore, they’ve allowed another person, with some intriguing issues of his own, to bring his problems into their space.