It is a loss, but a minor one, as most people who travel from Stockport use it as a "parkway" station and can easily switch to the new Manchester Airport one.
The loss will be to people who normally walk or cycle to catch London trains there. That is, on balance, an acceptable loss, but I think we should acknowledge that it is indeed a loss, just one outweighed by the benefits.
Similarly Coventry will lose its 3tph fast to London, which is a loss too, but similarly those using it as a "parkway" can switch. However, again, the gain outweighs the loss, and Coventry doesn't justify those trains alone, like many stations (e.g. the quieter ones on Merseyrail) it receives the service it does because it is operationally convenient to do so.
You can't make an omelette without breaking eggs, but it doesn't mean we shouldn't recognise downsides too, and perhaps look to mitigate them with e.g. quality bus services as
@Starmill suggested.