Unless your agency wants to take a symbolic stand against Apple then there are plenty of currently sold Macs that have passed EPEAT certification even if they are not currently listed.
As I stated in the first thread on this issue, I think Apple is moving to a new design that is more iDevice-like and therefore will continue to make further EPEAT certifications impossible. Therefore they being proactive about retaining the control here.
How many is 40%? How much profit is that really for Apple compared to the retail priced for the millions of consumers that might not buy a Mac because a competitor is making a better system that they can't compete with while trying to maintain EPEAT ratings across their entire Mac line? Let's not forget that other vendors have a vast number of models compared to a very small number of SKUs from Apple
If anyone is negatively affected here it's the users that rely on Macs in an agency that doesn't want to admit how outmoded EPEAT is or the hypocrisy that they don't require it for other devices. I'm guessing that eventually the desire for Macs will win out before Apple's desire for a few government sales.