Yes and no. Mostly no, but more yes than one might be comfortable with.
At the start of this century, Mikami was upset with Sony. He got a PS2 devkit in preparation for a new generation of Resident Evil and he did not like what he had to work with. As far as he could tell, his team would have to code to the metal to make the games he wanted to make. So he goes to Capcom executives and, as the creator of Resident Evil, has significant cachet within the company and got to make the call on his series. Mikami at this point decided to hold a meeting with Microsoft, who had been knocking on Capcom's door for almost a year at this point. Microsoft was willing to bend over backwards, but the way they ran the meeting intending to court Mikami actually ended up pissing him off. They had no idea how to deal with Japanese developers and their body language, people interrupting him, talking over him, as well as their lack of direction on what they wanted games to be caused him to stand up, bow, and leave the meeting before the end. He was at Nintendo's door soon and Capcom decided to trust his call.
Parallel to all this, Inafune was rising up the ranks as a producer within Capcom. He was making calls that were moderately successful to fully successful, he went out and worked the interview circuit, Capcom was happy with him. Inafune wasn't terribly happy with Mikami's Resident Evil decisions, though, and made this clear to Mikami. This caused some friction and simultaneously pushed Mikami to make the best RE4 he could make to prove a point but also double down dramatically on his decision. Ergo, "I will cut off my own head."
The thing is, Inafune was right. And Capcom knew he was right. Inafune earned a lot of credibility when REmake came out and bombed, killing plans for REmake 2. He was made a corporate officer and established as the producer for Resident Evil 4 PS2. In 2005, he was promoted again to Senior Corporate Officer and ended up saying yes or no to projects given to him by former colleagues.
All of this is important because you need to understand where Inafune's mind was at in 2005. He was repeatedly promoted because he was right about financial decisions and other people were wrong. People who were making decisions based on their gut or emotions were incorrect and he was correct and that's how he was going to change the industry. In some other people's words, he was a businessman, not a creator.
So parallel to all that, Clover was Capcom's prestige brand that began as Team Viewtiful. They were the tip of the spear of Japanese development, uniquely Japanese things that Capcom's best designers could make. Viewtiful Joe was this pseudo-hollywood, half-sentai game that split the difference and appealed to no mass market, Okami was super Japanese, God Hand was Japanese-wacky making fun of the west, these were not international games. By the time Inafune became a SCO, he had gotten a look at the Xbox 360 and saw that the days of the super Japanese game were numbered.
During the development of Okami, Inaba was making a similar gambit to Mikami's. It wasn't about console, but he was asking Capcom brass to trust him, that he would make sure Okami was successful even despite its long development time and seemingly limited appeal. At the end of the day, this gambit was what lead to the dissolution of Clover. It didn't work and Inafune signed off on it, believing that Clover's brand of game had no place in the coming market.
So it's not that Inafune marched to Inaba's office and fired him, Mikami, and Kamiya. But he definitely created an atmosphere where failures were punished harder and none of his former colleagues were happy answering to him as their superior. They didn't feel he had the love of games as his motivation and didn't like what he was trying to do with Capcom. In short, "You've changed, man."
It was a bad situation all around that stretches back fifteen years.