Merlin is impersonating Lancelot (which would explain how he was able to be in LWM as the 'usher' to warn young Emma not to pull the sword out of the stone).
As been pointed out by others, magical using villains often disguise themselves as others to trick the heroes. So, perhaps King Arthur and Guinevere are also disguised villains (Mordred and Morgana perhaps) which would explain why they don't want the Storybrooke heroes to talk to Merlin in Tree form (and maybe the Tree is not really Merlin but the real King Arthur)? And Lancelot (or disguised Merlin) warning Snow that there is a villain (not the Dark Swan) in the kingdom?
Then in Storybrooke, King Arthur convinces his henchman to steal the magic items (and the non-existent bean) and make the ultimate sacrifice in Storybrooke's jail to convince the heroes that Arthur is a good guy.
Rather sketchy for a hero king... Maybe Emma hasn't truly become dark and murderous but is playing a long game (and at the end of the 6 missing weeks, it's revealed that she had to cast the dark curse 3 to save everyone... like Snow casting dark curse 2).