On the one hand, it would make very little sense to lie about such a thing if you look at it on face value. On the other hand, rumors that an Avenger may be killed, or be evil, or be mind-controlled, would be explained quickly and easily with a Skrull replacement. Early rumors that Cobie Smulders would be playing not only Maria Hill, but the Skrull Princess Anelle as well, would be vindicated. Casualties along the way could be faked because the person killed could turn out not to be him or herself.
These are all potentially huge plot points and, while studios generally stand to gain little from hiding the identities of the central antagonists, they stand to gain substantially more by keeping major plot points and story twists under wraps for as long as possible. It's widely believed that The Avengers' biggest summer competition, The Dark Knight Rises, has been fibbing a little bit about the identities of certain characters all along so as not to spoil the story for know-it-all comic book fans.
They could even go the Captain Marvel route and have a Skrull replacement for [insert hero name here], who develops a conscience and has to sacrifice himself in the end.
In addition to getting the fans all riled up, there are other things at play here, too. If they are indeed flat-out lying in order to protect the movie's plot or maintain suspense, what does that mean for The Mandarin?
Iron Man's arch-nemesis and arguably the most cinema-friendly villain faced regularly by Ol' Shellhead in the comics would be a perfect fit for Ben Kingsley, whose suave brand of villainy has been chilling veins in films like Prince of Persia and War, Inc. in recent years. When it came out yesterday that he was in final negotiations to star as the villain in Iron Man 3, many fans took it as silent confirmation of long-standing rumors that The Mandarin would be the film's villain, but filmmakers were quick to quash that rumor, pointing to studio comments that the movie is loosely based on Warren Ellis' Extremis story as a way of proving their point.
And it sounds totally reasonable, and nobody much has any reason to doubt it (although MTV still kind of does). After all, there's no really good reason for them to lie about something like that.