The attacks made by the detached units of 7th Air Force were very much according to doctrine. When the B-17s attack the Midway and Kure invasion forces on 3 June they did so from somewhat lower altitude than they were to on the 4th; I want to say between 8,000 and 12,000 feet. Despite attacking slower moving ships without fighter cover, the B-17s score no hits while suffering damage from Japanese AA.
When Sweeney and crew landed at Midway, they thought they score a number of hits that damaged or destroyed a number of ships. They were also surprised by the volume and accuracy of the AA fire they encountered. As a result, they decided when the time came to attack KIDO BUTAI they would do so from a higher altitude. This would reduce the number of hits, but they felt they would still score. It would also better protect them from AA and fighters. While we know the B-17s didn't hit anything on 3 June (which is why in hindsight we question what he did on the 4th), Sweeney and his men thought they did.
So the first take away to make is: based upon the information at hand, wrong as it was, there was no need to radically depart from established doctrine. Had Sweeney brought his men in at 500 or 1000 feet, lost a bunch of planes and failed to hit anything his superiors would be wondering what the heck he was thinking.
Also keep in mind a group of B-17s did make a rather low level attack at Midway. Between 1800 and 1830 a group of 6 B-17s dispatched from Hawaii bombed the damaged HIRYU and her escorts from 3500 feet prior to landing at Midway with no better results. They attacked from low level because they lacked fuel after their long flight to climb to a more doctrinaire altitude, and their lack of results show hitting moving ships is hard no matter the attacking altitude.
Would a low-level attack have worked? Maybe, but it would have been 100% improvised, 100% against doctrine, made by pilots who had never been trained for such an attack, and it would have brought KIDO BUTAI's combat air patrol into play when it barely when they attacked from 20,000 feet. I personally feel all of those things work against a successful attack, but maybe it would have worked.
Hope this is helpful, and hopefully the typos have been kept to a minimum.