Yonai would represent a different military faction

Could a civilian counter-coup in Japan in 1941 change policy without being overthrown in turn?

There is no firm answer. The emperor's support could help, while Yonai's naval background would make his rise a change of military faction.

The survival of such a government remains uncertain. The emperor's support could give it a chance, but Mitsumasa Yonai belonged to the Navy himself. His rise would therefore put a different faction of the armed forces in power. Following that change through Japanese politics would require too many additional assumptions for the scenario, which stops with the Allied position in the Mediterranean and Atlantic in 1941.