Whedon's contribution to the film's success is universally heralded. Without his dialogue and pacing the film loses some charm. The gamble would be will people show up for the sequel regardless? Can we turnover Whedon and worry about Avengers 3 at a later time.
Marvel--this isn't the time to gamble. Yes, people are going to show up for TA2 but they will expect the same type film they got. New people in charge of the script and directing will be noticeable.