I'm devoid of sympathy for this TSO. That said, if he didn't really know what the pen was worth and thought it was just a pen on top of a filing cabinet, a felony conviction does seem a little steep. I personally think a misdemeanor conviction would strike the right balance. Had he actually taken the pen at the checkpoint knowing it belonged to a passenger, then a felony would seem like the way to go. Frankly, I'm okay as long as it results in some conviction and record.
If I forget that I have a loaded gun in my backpack I get a felony conviction at the checkpoint. Doesn't matter if I forgot it was there. They are the ones with the zero tolerance rules, not my fault if they get caught up in them.