The Autobots would never willingly fight humans, even superpowered ones - in most continuities they're usually under orders from Optimus to protect them at all costs. If the Autobots did start exchanging fire with superhumans, Jazz would have iced Circuit Breaker upon her first appearance in the Marvel U.S. comics; just based on their size and firepower, the Autobots could kill a third of the Marvel Universe if it came down to it (let alone what the Decepticons would be capable of).
That's not to say the Autobots would never attempt to reason with any superhumans that crossed their paths, but then knowing the Avengers as they are even pre-Civil War, it's not like anyone but Cap would be willing to listen until major damage was already done to the Autobots. B'sides, the government would have a say in what happens to the Autobots too since they monitor the Avengers' activities; remember what happened when Vision went all wacky back in the '80s. I won't even bring up what happened to Bumblebee in that horrid excuse for a G.I. Joe/Transformers crossover that Marvel published...
