The firing of Tamogami casts serious doubts on the sincerity of the Japanese government to make amends for Japan's aggressive role in World War II. One does not get to be the ASDF chief without strong political support, so it is only fair to assume that the general benefited from the strong backing of highly influential politicians over the years. Therefore, it is also fair to assume that some political leaders have silently condoned the general's views while simultaneously singing another tune to the international community.
By allowing Tamogami to retire with full benefits, the government sends a subtle signal that it condones his views. Firing the general from his position makes it look like he is being sacrificed merely to appease the international community; other than that, it is "business as usual."
I wonder how many more Gen. Tamogamis are out there among the ranks of the Japanese military, and how many supporters they have in the government.