Whenever a Starfleet captain bended the PD, he or she had ample reason to do because the case was ambiguous. Guys like Captain Merik or Admiral Dougherty on the other hand would have been court martialed for clear violations of rule number one.
The Federation citizens who are forced to move after the Federation-Cardassian peace treaty can protest against the decision, gather support in the Federation and influence the decision process. When you make democratic decisions there are always winners and losers, yet this cannot be compared to outright criminal behaviour. One might consider the price for peace to be too high, but giving up land for peace is anything but criminal.
The viewers who don't accept Picard's perspective are free to side with Dougherty, but I like to point out that he ended up on the face-stretch-bank.