I think some folks are blowing this whole "Rowling would never sign off on the Ministry being accessed through Diagon Alley because it's not that way in the story!" thing just a little out of proportion.
Sure, she may well be that kind of a stickler. However, practical compromises are always going to be required in the translation from page/screen to a real world environment. Hogsmeade isn't 100 yards from the entrance to Hogwarts in the source material, either, nor does the Hogwarts Express platform dump the students into the streets of Hogsmeade.
If Universal feels they can make a compelling logistical case for why the Ministry should be seen as part the overall Diagon Alley area, I think Rowling would listen to that. Personally, I'm expecting the Ministry (if it's built) will be accessible both from inside Diagon Alley and from another pathway outside of it. I think that makes the most sense from a guest flow perspective.