Moriarty didn't trick Molly - she knew exactly what was going on when she started dating "Jim from IT." She actually helped him cover up murders on a number of previous occasions. When Sherlock came to her for help with his "final solution," she and Moriarty had a whole plan for how she could help Moriarty kidnap Sherlock while he was incapacitated and then they'd have him at their mercy while nobody was looking for him because they thought he was dead.

John and Mycroft figure this out and do what they can to stop Molly and Mycroft. Part of their plan requires not telling Sherlock what's going on (just like Sherlock wasn't telling John about his own plan). John is still hurt that Sherlock would keep something like that from him. Molly's plans are all thrown off when Moriarty goes and actually kills himself on the roof, though . . .