Things that don't make sense (v2)

1) Many of the crew leave before the Collector attack. Remember that it happened one month after the attack on the Citadel, and Wrex himself asks how the Normandy was doing when meeting with him on Tuchanka. After Saren is stopped, there's no need for the crew to stay together, since the goal has been completed and they specifically told you that they would help you in the fight against Saren, and the Alliance was mostly doing some cleaning of the remaining Geth holdouts. Garrus went back to C-Sec, Wrex to Tuchanka, Tali to the Fleet. Ashley/Kaidan were still part of the Alliance and Liara didn't have anywhere to go, since she joined the crew not with the promise of fighting Saren and could be there to further "study" Shep and his/her visions.

2) The problem wasn't contacting Shepard, but the guy told Hackett that he would be placed under a somewhat-formal arrest for supposedly evading the Alliance for those 2 years that Shepard was dead.

3) This was a one-time only and they were never told that Cerberus used them as bait, only that Shepard was involved with Cerberus.

4) Remember that Cerberus were still the "good guys" from a certain point of view. See Star Wars for example, some people don't really know that the Empire does nefarious things, and serve them as ways of doing things right when no one does. Cerberus was just that. When the Collector Base was destroyed/saved and The Illusive Man studied ways of defeating the Reapers, he adopted harsher methods. Folks could be onboard, (un)knowingly.