Hulk is on the run. He isn't suddenly a good guy. When Stark approaches the General at the end of TIH, he mentions a team he's putting together. I really doubt that the "team" is meant to include Hulk...it's likely meant to take down people and creatures like the Hulk (ahem...Stark buildinig the "Hulk Buster").
Banner would probably only be a temporary "villain" in the beginning of the ...



