It puts Hiroshima alongside the Nazis and the sinking of the Lusitania, which he also tries to stop. Was the prevailing opinion of the bomb unfavorable by this point? Would this episode have been very controversial? How did public opinion on the bombing shift in the first few decades?
Also, as a side note, the Japanese police officer he talks to says "I think we can handle one B-29;" is their knowledge of the incoming plane at all accurate?
The atomic bombs were always polarizing, though the percentages on each side of the "issue" varied over time. By the 1960s you did have significant numbers of Americans who thought that the atomic bombs were excessive, and at the very least even if they were "necessary evils," that the loss of life was tragic. I don't think it would have been viewed as "treasonous" but certainly Rod Sterling's politics would have been relatively transparent (as they were in many of his episodes, a large number of which were explicitly political). It would have been the sort of thing that a liberal-left crowd would have resonated with, the same audience for Dr. Strangelove and Tom Lehrer songs and so on — white, middle class, educated, not so hot on the arms race, dubious about conservative anti-Communism (not quite rejecting of liberal anti-Communism). Liberal, not radical. (Vietnam would change the politics on this as with many things among the US left.)
By the early 1960s these kinds of thoughts were no longer regulated to people on the far-left or associated with a pro-Soviet line, they had permeated into the "liberal consensus" mainstream. My guess is that it would have been seen less as "controversial" and more as "edgy," to use our present terminology.
I did a quick ProQuest Historical Newspapers search to see if any press had been generated about the episode. Nothing popped up other than routine summaries. That doesn't mean nobody talked about it, but it never bubbled up to the level of major national newspapers.
The best books on shifting US attitudes towards the atomic bombings are Paul Boyer's By the Bomb's Early Light and Spencer Weart's Nuclear Fear.
As to the second question, the Japanese had some radar and other bomber-detecting technology and were aware that B-29s were coming in. There was even an air-raid warning at Hiroshima for the weather plane that preceded the Enola Gay by a few hours, and was lifted before the actual attack. So the Japanese were able to know that there were lone B-29s going around many places in Japan, usually conducing reconnaissance. As for knowing it was a B-29, by that point in the war the Japanese had gotten very familiar with "Mr. B," as they called them, as they had a very loud and distinctive engine, and the Japanese learned that if you hear "Mr. B" coming, you should probably get into your bunkers.
But the more accurate statement would not have been "I think we can handle one B-29," because the Japanese were not in the business of chasing down lone B-29s at that point in the war (both because lone B-29s were usually well-armored and well-armed high-fliers, and because the Japanese air forces were deeply depleted at that point). A more accurate statement may have been something like: "How much damage can one plane do?" When they worried about B-29s they worried about mass attacks that dropped incendiaries, hence the lack of any kind of evacuation or air-raid preparations when they only saw the atomic bombing planes, which were indistinguishable from the other lone B-29s that were seen daily over Japanese cities.