See, here's the thing. Cover going public means they are in a transitional phase, and the way they're transitioning is that they need to go from a "small tech start up that got lucky with some good talent hires" to a a company that is a safe long-term investment, and in order to do that they need to grow the image not of one that's good because of the talents, but a company where the talents are good because of the company. And the way they are doing this is with live concerts, sponsorships, collaborations, all things that are visible to investors in easy to understand ways. It's not just about entertainment anymore, the company needs to assert that it's not going to collapse just because some talents leave, that they can recruit new talents and make them just as visible. For that, the talents who play along with the company's direction are needed more than the ones who want to showcase their own talents and ideas.
Someone like Ame is actually a major threat to this image. She's an atypical talent who captures the public mindshare due to her own ideas and technological skill. She's an anathema to the idea that it's the company that makes the talents great because she insists on doing things without the company's help. Thankfully for Cover, their investors only have surface level knowledge of Hololive and this goes even moreso for EN. If they realized some autistic girl was able to set up her own studio and pay some SEA slave to produce a live concert all on her own, they'd start asking questions like why Cover needs a second studio or why they need so many staff members.
So Ame had to go. They would diminish her mindshare by giving her less and less opportunities. They restrict her normal streaming activities in small ways and restrict more and more of the things she used to be able to do to make her feel more and more stifled, resulting in her streaming less and less until she disappears from public consciousness. Then she finally gets fed up and quits on her own in order to start doing her own thing. This is classic Japanese corporatism. You see this happening to creative minds within game studios all the time.
