The reason JJ makes it seem that Vaughn is a bad guy is to build suspense between Vaughn and Sydney. I mean it wouldn't have made sense if they just lived happily ever after...as much as some of us would have liked it. By showing that Vaughn could possibly be married already creates a sub-plot (in the producers eyes at least, in ours it'll always be the main plot) for next year, with the main plot being the rambaldi device.
