I must confess to not being terribly comfortable with Coulson being alive either. He seemed pretty sure he was going to die. Fury seemed to think he was dead. And the motivation the team had to take on Loki and win came in large part from having something to avenge -- a point made in the movie.
I don't know. It just kind of cheapens Coulson's big moment, as well as a signigicant part of the plot -- not to mention Tony's awesome "His name was Phil" line.
Maybe they'll make it more than just a cheap deus ex machina and have some ongoing mystery revolving around his death/return.