The focus screen in the 7D and all auto focus cameras are designed to be bright with a slower lens like a zoom that doesn't open more than say 5.6. That way the viewfinder doesn't darken up. The problem is when you do that with a fast lens it is sometimes hard to see what is in focus and what is not, due to everything being so bright. When you put a screen in the camera for fast lenses and manual focus the slow lenses get very dark and hard see through the viewfinder. I just checked and the 7D does not have user interchangeable screens so that is not an option.
I don't know how much you looked at Zeiss's website about the focus shift but basically the AF system always looks through a lens like it is a 4.0 or slower lens and on very fast lenses which are not corrected the focus shifts forward slightly when you stop down. Problem is when build a lens with the corrections for fix this problem you loose some of the look and feel the lens gives you.
The 50 1.4 and the 85 1.4 are the only two Zeiss lenses that work like this. All the others work fine at all apertures with the AF assist and on my 5Ds work very well. Come to think of it I haven't heard anything one way or the other with focus shift on the new 35 1.4 so not sure on that one.
If you think you may have a problem get the MP50 or the 35 2.0 and you will be fine. I just don't think those lenses have quite the vintage B&W feel that the 1.4s do. But then again my MP 100 can do things my 501.4 can't and vise versa. There is no perfect machine!!!! But as they say if there was a perfect machine we "couldn't separate the men from the boys".