Idk how you could look at GNOME and say its trying to act more like Windows. They have their own particular idea of what a desktop should be, and that might not include middle mouse pasting. Defaults shouldnt stay the default just because they've always been. Devs should be able to have discussions about changing things without people accusing them of trying to destroy Linux.
Edit: I also want to point out that a huge number of Linux users dont even know this is a feature (some of which you can see in this thread). This change will add an entry in the settings for it, which very well might lead to MORE people using it. I think disabled is the correct default for something as potentially dangerous as dumping your most recently highlighted text.