There are NO legitimate reasons not to let a Wiccan put a pentacle on their memorial plaque. I don't know who the VA think they are making a judgement about the legitimacy of a fallen soldier's religion, but they need to have a little compassion.
As an aside, I wonder if atheists get anything on their plaques? Agnostics should get a big question mark. :)
I see two possible reasons here.
The first and most likely is a simple slow bureaucracy. Nobody thought to have that marker yet, and the gears will turn slowly before it happens. To paraphrase, never attribute to malice that which is more easily attributed to bureaucratic inertia.
Far less likely, somebody in the VA is an ignorant Chrisian bigot who doesn't want to have the "symbol of Satan" defiling American cemeteries. And somebody needs to be fired.
I suspect that by the time they need a grave marker, they are no longer agnostics.....