It's possible that this was Apple using their weight to change the standards.
And if they were doing so, then ultimately they acted in the best interests.
Here's a key quote from EPEAT CEO Frisbee:
"We look forward to Apple’s strong and creative thoughts on ongoing standards development."
That insinuates that Apple approached the Green Electronics Council to make certain changes to EPEAT. It is likely that Apple's suggestions proposed for more stringent criteria and would have disqualified many products from the competition.
Or heck, it could have been something like "let's use EPEAT on smartphones and tablets." What if other handset manufacturers had that dropped in their laps and they weren't ready for it? Would it be likely that they would protest to the Green Electronics Council?
If the Green Electronics Council balked at Apple's proposals, then Apple forced their hand by withdrawing. Losing one of the biggest consumer electronics companies on the planet (and one which helped drafted the original EPEAT) was probably too much for the Green Electronics Council to stomach.
We'll probably never know the full story, but my hunch is that Apple called the Green Electronics Council's bluff and the latter folded.
We can only see the heavily sanitized public statements, but Frisbee's comment pretty much says that Apple will have a more prominent voice at how EPEAT evolves.