I am glad that they reconned them from both connections actually. In my mind, they were created in an Avenger comic for the Avengers. The Magneto connection came later. Since the Avengers came first in the creative sense, their lience should lie with the Avengers, so I side with Marvel and Disney with that.
Peter Parker's parents were Shield spies, but that didn't give Sony any right to mention THAT little tidbit of information in any of the Previous Spidy movies. Maybe now that could be different since Sony and Dis-Marvel are on good terms.