Variety Reports on Why MacLaren and the WB parted...
http://variety.com/2015/film/news/wonder-woman-michelle-maclaren-wb-1201473481/
In short, they just didn't agree on anything.
Doesn't mean either vision is wrong or right, just that they weren't the same and when the purse strings and the helm can't agree, it makes sense to part.
Specific points of contention raised:
- MacLaren wanted big budget action, the studio doubted her action chops and wanted a character piece
- The studio liked Fuchs (and 5 other) treatments over MacLaren's
- MacLaren was inexperienced in dealing with big-budget production
If preproduction, less action, and budget were part of the sticking points, then Snyder's alleged preference for the Crimean War is unlikely to have pleased the studio either (compared to WWI), so the separation is unlikely to do with a difference of opinion with Snyder.