Well the Netflix shows were always promoted as being part of the larger MCU, at least peripherally. I don't believe Feige has ever come right out and claimed they were in their own universe. I think both D'Onofrio and Cox both being in a 'canon' MCU show and movie basically confirms their status. Besides, it's pretty much a non-issue when you think about it. Just carry on with the characters. The MCU doesn't necessarily have to reference what came before. If Kingpin and DD ever met up, just have Kingpin say something like "nice to see you again" while winking and move on from there. It could mean multiple things, while still providing an Easter Egg to the Netflix show fans.