Well they're heading for Akatsuki's base, so they should expect a good number of Akatsuki members to be there, and have no knowledge that they're just in their shadow forms. If I were in the Konoha teams, I would assume the badguys used the meat pupper jutsu to fight because the actual badguy is at the hideout doing something else, like lounging or cleaning his room. If the actual badguys are at the hideout, the goodguys are in big trouble.

Now if Jiraiya shows up, that would be a different story. But can they keep relying on an aged pervert with vices to save the day? Might as well expect the 5th Hokage to come to the rescue.