Yep, that's somewhat bad news in the short term for Middlewich. It's going to be pretty hard to sustain a business case for opening a new line and station, just so you can provide trains to Altrincham! Even with Metrolink available to complete journeys to Manchester, that'll be quite a deterrent to using the train for many people. (And I wonder how well used the new Chester-Altrincham train is going to be).
On the upside, I imagine the obvious idiocy of terminating a train at Altrincham is going to cause some political pressure to be put on the Government / NR / TfN to investigate infrastructure improvements to allow more trains - either more trains between Stockport and Manchester, or if that is too difficult, to at least allow trains to terminate at Stockport from the South (which would be a little bit more useful than terminating at Altrincham). Maybe if there were infrastructure improvements around there, that would make it easier to build a business case for Middlewich?