BobZilla 2k10
The elephant in the room isn't shepard as you put it, its cerberus.
What you seem to be missing in your interpretation is its the fact that Shepard is working with cerberus that creates most of the problems on Horizon.
If shepard had just returned alone or with some other ally on Horizon and then the VS. made the accusations that they did against Shepard then your interpretation would be spot on, but its the fact that he's working with cerberus that becomes the key factor.
What Shepard did 2 years previously has no bearing on what he may be doing now, simply working with cerberus opens up way too many questions, questions that apart from the VS. few people including Shepard himself ask or try to find answers for.
Shepard was presumed dead for 2 years, rumours were spread he was alive and working with cerberus, he arrives on Horizon and surprise surprise he's working with cerberus.
This opens up key questions, questions that Shepard despite having evidence to prove his position doesn't answer very well, in fact he's almost completely dismissive of these questions and answers with no proof other than his word, which the mere fact he's now aligned with cerberus puts his word into question.
Shepard makes a claim that working with cerberus is the only way to stop the collectors, does he provide any evidence or this or simply suggest that he's knows best?
We as players are completely aware of the whole picture, we know what's happened during the past 2 years, we know why Shepard's aligned with cerberus and we know that Shepard is still the same person he always was.
The problem is that by working with cerberus, by not offering any evidence or proof that this is the only course of action available, by the mere fact that he's alive and not explaining how that is the case, Shepard's position, his word and therefore his actions are all open to questions, questions that while we know the answers to are not answered to the VS.
Think of it like this, Saren was considered the top spectre in the universe, someone completely above reproach, yet he turned against the very people who trusted him most, so why can't this be true of Shepard also?
If Saren who for over 20 years was considered a legend, the galaxy's most fearsome spectre and someone who people looked up to can fool the people closest to him so much that Nihlus never expected the gunshot that killed him, then why could it not also be true that Shepard may be going down the same route.
His presumed death and resurrection, his being absent for 2 years, his alignment with cerberus (regardless of how he felt about them just 2 years earlier) all of these open up questions that Shepard doesn't answer.
Remember how the council acted when Shepard made his claims about Saren, they asked for evidence, only then did they believe the truth about him, so why should it be any different with the VS and Shepard.