I still think that, once the team comes to actually starting their matches next season, you guys will rapidly forget the MCFC link. For a few games you'll say "oh, that's the MCFC youth who set up that goal" or "you can see that they're trying to make this team play like MCFC" but I reckon after only a month or two you'll be saying "oh, that's our loan player who scored that amazing chipped goal" or "you can really see the NYCFC style of play shining through".
It's like American products over here. We occasionally moan that, say, the American burger culture is fattening us all up with all their McDonalds and KFCs, but 99% of the time, when I go to McDonalds I'm not thinking "I really want some American burger grease", I'm thinking "I quite fancy a hamburger right now". The fact that it may or may not be from the American food culture rather than the British one is a complete non-entity in my mind as I eat.
Yes, the link will always be there, and if you want to look for it it will never be hard to find, and to either praise or criticise depending on your inclinations. But if you stop looking for it, you'll forget it's there, and that's the way it should be IMO.