No, there's no evidence Widmore or anyone else other than Desmond knows anything about this other universe. We don't even know Widmore's plan for Desmond yet, only that it hinges on Desmond being able to survive a huge electromagnetic event. He subjected Des to a test, but doesn't appear to have any knowledge of what that exposure did to Desmond, where his consciousness went.So, Whidmore knows Desmond can handle the "power of the island" - in that he can go back and forth through both time and universes, but does he know his wife has a similar ability?
Eloise was described in the "Flashes Before Your Eyes" commentary as sort of a temporal cop. Out of all the characters we've ever seen on Lost, her power seems to me to be the greatest, rivaling even Jacob in knowledge of the universe. I mean, there's no real evidence even Jacob knew anything about the sideways world, so that places Eloise in an even higher position of universal knowledge. This is a big question mark that needs to be addressed, and I'm afraid it's going to be one of those things that goes by the wayside. I would rather have some explanation for Eloise and her apparent wisdom than even an explanation of the whispers, and that's a mystery going back to the first season.She knew all about Desmond and spoke to him in the episode where he was switching universes or time traveling or whatever he was doing when he turned the failsafe key.
She also knew about him last night when she warned him not to try to find what he was looking for.
I think she knows what's happening whatever the time line or universe or ... whatever.