Even if they manage to make their deaths look like an accident, it will not erase suspicion. In fact, it'll add to the suspicion. Nothing hides from the media. Word will get out that the men who died happened to be 9/11 conspiracy investigators. Plus, a video of 9/11 conspiracies being removed would add to the suspicion. Killing them would just make them a martyr to the cause and bring more supporters. And as someone put nicely, if a project has over zero people involved, word will get out eventually. Creating such a major undergoing in total secret with absolutely no clues that anything ever happened is very hard to do, maintaining the secrecy is just as hard. If "The government" has the ability to pull off 9/11, they have the ability to make it look like an accident without suspicion, and would have stopped the kids from ever finishing the film before it could be posted.