What I thought about it was that the jocks basically got together and voted for him. Lets say there are 3 major candidates for prom queen:
Adding in Kurt, that makes 4. Kurt would only need to get a minimum of 26% of the vote to win, given that everyone else got a roughly equal number of votes. That means that all of the jocks, who are pretty much pressured into hating Kurt, and are also under scrutiny for outward displays of hostility, had to find a different way of dealing with Kurt.
Lets say ALL of the jocks voted for him. That includes people like Finn who are on multiple teams, such as both Basketball (well last year he was) and Football, and people like Puck who are only on 1 sport. With all of the sports teams McKinley seems to have, football, basketball, hockey, and presumably soccer and/or track and field, that would mean that if every jock voted, Kurt would get WAY more than the needed number of votes.
That being said, it may have not been just the jocks. Remember what Puck said about anti-prom king? This could be the same people Puck was talking about who vote for the anti-king, but taking it in a whole new direction. The reason no one laughed was because that would give it away that there was something amiss.
Either way, the silence was more than likely the audience going "holy crap that worked?"