All of the war criminals were released and pardoned at that time. Basically, there was widespread belief in Japan that the war crimes trials were unfair because they were trying people for things that weren't crimes at the time they were committed. It was victor's justice with ex post facto laws, went the argument. There was also the feeling that the trials were racist--there was anger that all of the justices presiding over the trials were white, with the exception of one hastily added Asian, Justice Pal, who was the only justice who found everybody not guilty, because he questioned the legitimacy of the war crimes trials.

In this context, when the US Occupation of Japan ended and disposition of the war criminals was given to the Japanese government, everyone was pardoned and released. There was nothing specific in this situation to the Unit 731 members--the pardon was across the board. The only thing that distinguished the treatment of Unit 731 members from other accused war criminals was that most never had trials. The US made a deal to release them and not try them for war crimes, if they shared their data with the Americans.

I do believe it was because they shared their research with the US government in return for amnesty but I have no source for that, just remember reading it once.