I must agree with the opinion that the Communists winning so many votes seem very unlikely, at least a majority. A plurality might be possible in some scenario. If something like was to happen, there are ways how Americans and the SCAP could attempt to fight back. Prior the election, Americans could prevent some people becoming candidates and put restrictions on the Communist campaign activities. They could also attempt to influence other Japanese parties to work together, so even if the Communist gather the plurality of votes, some other parties might be able to create a governing coalition. They might even attempt to purge people who become too difficult to deal with. At the same time though the US would probably prefer to keep their influence invisible, if possible. It should be also kept in mind that during the Occupation, it is the SCAP which holds the sole executive authority in Japan, so even if the highly hypothetical government led by the Communists opposes Americans, their freedom of action is rather limited, if the US chooses so.
It should be noted though that Americans might be ready to at least attempt to work them in 1946, later this becomes more difficult. At the start of the Occupation Americans and the Communists had still relatively good relations and had extensive cooperation during the initial reform period. Americans even seemed to like Nosaka, even if they distrusted other Communist leaders.
The U.S. would be miffed, but owing to the nature of the JCP, might tolerate them. Memories of the Pacific War were still fresh in 1949., and JCP was decidedly pacifist-at least there was no danger of Japan rising up and waging wars around Asia with Nosaka at the helm. He was not much of a Soviet stooge anyway, from what I know. Of course, a neutral, disarmed Japan cannot serve as a bulwark against actual Communist belligerence.
By 1949, the Communist Party was clearly seen as a hostile political actor by Americans. Although the rearmament drive hadn't yet started, they were already moving towards the position where earlier disarmament policies were seen possibly too restricting. There were American officials already complaining in 1948 that some decisions made regarding disarmament were too extensive.
Article 9 was a Japanese idea.
We actually don't know whose idea it excactly was. Two most likely candidates are either PM Shidehara or MacArthur, though there were others who had suggested something similar before. It's worth noting that the Filipino constitution had somewhat a similar article in it, so it is likely that MacArthur was rather familiar with the idea. He seems to have had some sort of grand vision of Japan as Asia's Switzerland, though unlike its European counterpart, disarmed.
With regard to a Socialist-Communist coalition, remember that the Socialists themselves were deeply divided between a left and a right wing, and were soon to formally split. (That alone is enough to make the Chile comparison invalid.)
^This. I don't see even all Left Socialists being particularly happy about forming a coalition with the Communists.