I hear what you're saying, liv. And it's not the first I heard of behind-the-camera-shenanigans causing Michael Pitt's ouster. But, still...
Jimmy did try to have Nucky killed. Jimmy did supplant him as King of AC. And Jimmy failed miserably at it. He lost all respect from his supposed comrades. Even his civilian underlings didn't give him respect. I doubt that Uncle Jun would have continued to act as his consigliere.
Jimmy was done. Even before Angela's death, Jimmy could not hold shit together.
As for Nucky, he needed to do this...he couldn't be half a gangster. Yes, I've lost a lot of sympathy for him, but are we supposed to feel sympathy for him? It's like Tony Soprano, a lot of the time you forgot that he was vicious, dangerous brute.
Don't get me wrong, I loved Jimmy. And, in truth, I wished he did kill the Commodore at the outset. But, he didn't. Right there and then, his fate was sealed. Even if Nucky didn't kill him, but granted him exile...Jimmy would still be off the show.