The only nation capable of beating IJN was the US Navy. Absent of the Japan-USA war, Japan's empire of survivability increases.
With regards to gekokujo, the only person that can stop this is the Emperor both de jure and de facto. the Meiji constitution proves that civilian authorities are separated from military power with the exception of the emperor.
Now if the emperor will act is a bit of a question. If the Emperor really wanted this to happen, there is plausible deniability. In the end the emperor can always order seppuku and disgrace these insubordinates if the Emperor wanted to act something about it. Besides, the Meiji consitution proves the emperor that leeway to do such a thing.
The great thing about gekokujo is that it was rampant during the Sengoku but seems to be almost non existent in the Imperial period upto the 1930s.