The fact that the naming convention has existed "for years" is beside the point - clearly it hasn't been in widespread use by many others, and GNE's resulted immediately upon recent introduction.
Yes, SOPs should have caught all errors but they didn't.
We know that it does no good to simply implore that SOPs be "followed" because people make mistakes. Otherwise we wouldn't have AF447 and a ton of other accidents which the adherence to SOPs may have prevented.
One of the easiest mistakes to make when pressing the FMC keys is a transposition of characters. Usually that is caught right away either because the FMC doesn't accept the sequence or the other pilot is watching. If not caught there, checking the flight plan tracks and distances at each waypoint is the SOP that should catch it, followed by the standard checks at each waypoint passage while enroute.
As your experience illustrates, it isn't the naming convention that is the problem. It is familiarity, which perhaps means that this particular change was too quick, and/or not properly described in manuals?