Hawkeye has always been seen as a capable leader as far as I can remember... and that's since Avengers No 44--the original Red Guardian/Black Widow/Bamboo Curtain story line back in the 60s. It depends on the writer.
I agree, Hawkeye has the leadership capability. However, I think the point being made is whether or not he is the best to lead a covert squad. I have to say that he probably isn't... and that Mockinbird (who has the training, the contacts and already leads a covert operation with the WCA) would make more sense.