What the Head Judge of an event says, goes. In theory the Head Judge has the authority to toss out the rulebook completely if (s)he so chooses. Granted that's likely to provoke a (justified) TO revolt and said HJ probably won't be contracted to do events for a while, but they can still do it. Ultimately, what you think a player should and should not be DQed over is irrelevant - the HJ decides what is DQable at their event and not.
As far as what you should do? If this is a floor judge, then it would be entirely reasonable for you to take the issue up with the HJ - I'd advise that you do so politely and discreetly. If it's the HJ, you're going to have to let it go for the event in question, but you can make an inquiry with your relevant Regional Coordinator. If the HJ was in fact in the wrong to an egregious extent, the RC will take whatever educational or disciplinary actions are appropriate.
EDIT: +1 to the above poster. You should maintain professionalism by resolving the issue in private away from the table. I'd also recommend doing as the prior poster says first, before going “over their head” to the HJ, just as a matter of courtesy.
Edited Colleen Nelson (Oct. 24, 2013 05:41:31 PM)