Weirdly, the entire plotline highlights a bunch of things.The sheet of paper she burned says that Merlyn was the client, so she's the one who planted the bombs for him.
* Papa Queen was a piece of crap
* Papa Queen completely misread Moira because she knew about his cheating and is much-much smarter than him by all accounts
* Moira probably would have happily had Dad pay Emiko off. She wasn't exactly Catelyn Stark but gave a 1 million to get rid of Oliver's "bastard."
* Dad was already at that time involved in terrorism.