Tyrion and Varys both advising Dany doesn't feel right.
It could happen, I guess, but I think the notion of Varys secretely returning to work from the shadows against Cirsei has even more potential on a TV show than in the book, so my guess is that they won't get rid of Varys for now.
My guess is that they were looking for story arcs they could cut completely. If they don't have Lady Stoneheart, and they don't send Jamie to the Riverlands, they may be tempted to get kill off Brienne for instance.