It's unfortunate that we don't see Bruce Banner discussing anything of the climactic battle afterwards, as it is still unclear how much he recalls of his time as 'the other guy'.
It seems that Banner has limited control over the Hulk, or that the Hulk retains a limited amount of Banner's personality. This seems to be related to the amount of focus or preparation Banner takes before turning.
As we saw at the end of The Incredible Hulk, Banner could exert a serious degree of restraint on the Hulk when he had both focus and a goal. He was able to create and at least partially control a transformation at the end of the movie, and he was able to give the Hulk focus and a target when up against the Abomination.
On the Helicarrier, Banner didn't prepare or expect his transformation. He wasn't sure what was going on, and he didn't have a target to focus on. He found himself facing Black Widow, who treated him like a threat (rightly so). Black Widow became the focus of his newly-transformed brain, which was filled with anger and uncertainty. Early in the fight, you can see Hulk is not really clear on what is going on - he's not going after Widow full bore, but more because she's there and a threat.
Once he fell, he had time to calm down a bit - his enemies were out of reach, and only the ground was threatening him. The parts of his mind that were still Banner were able to give him direction - hurt no one - and he was able to steer his fall appropriately.
In the battle in New York, Banner had a clear goal, a clear picture of his enemies and allies, and was well prepared for his transformation.
You could consider the Hulk similar to a well trained special forces soldier - give him a mission briefing, parameters, and a go signal and he'll do his job to the best of his ability. Jump him in an alleyway, and he'll react instinctively (which, for most combat, means 'with intent to kill').
