If a ton a viewers stopped watching the show just because Vaughn is married, they're watching for the wrong reason. Alias has much more to offer than a little perfect romance where nothing goes wrong. The only bumps on the road were times of disagreement and mistrust. But after a while that would get boring--the main reason why they started dating in the first place: JJ said he would be sick if there was another episode of "I want you but I can't have you," which was present in Season One and early Season Two. The same would happen if they just exchanged a kiss every episode--it'd get boring. There has to be drama in it because, well, Alias is a drama.
Although I'm sure that ultimately Vaughn and Sydney will be back together, I don't mind seeing them thrown off course. There's much more to see in Alias--spy action, family interaction, Rambaldi mysteries, and the suspense and plot twists that come every episode. The S/V relationship is only a part of the show. With or without it, Alias is still a great show.
Not to mention that it's uncharacteristic of any Hollywood professional to throw a straight out lie, and then another professional to confirm it as a spoiler to the public.