What can we do about this? How can we prevent the physics community ressponse to certain questions being screwed up like this? How can we avoid that powerful people at superior positions in the overall SE network get a wrong picture about the needs of OUR community and in the worst case take wrong actions against users who do great contributions to physics SE?
Nothing. If you don't want the visibility and exposure, don't post on Meta. This is a public Q&A site, not an exclusive country club.
As I mentioned in a comment to the post you're citing specifically, this is not a physics-specific issue. It requires absolutely no knowledge of the subject domain. Rather, this is something that concerns the Stack Exchange engine that runs all of these sites:
These aren't physics-specific issues we're talking about. They're first and foremost social issues, and secondly, issues regarding the operation and ideology of the Stack Exchange network, on which this site operates. The fact its topic is physics is quite irrelevant to any discussion of its policies and procedures. As someone who is a diamond moderator on 2 sites, and holds upwards of 10k reputation on 2 sites, not the least of which being Meta Stack Overflow, the Q&A site for the Stack Exchange engine itself, I'd say that yoda is perfectly qualified to be answering this question.
Your position appears to be that only the "expert" users who participate on the main site should be eligible for commenting on the meta site. In fact, I'd argue that you have that backwards. The "experts" on a meta site are those people who are experts on the Stack Exchange engine and the policies, procedures, and norms that apply across the entire network. I'm not sure where else you'd look for those people except for SE staff members and community moderators on other sites in the network. Objectively speaking, we're precisely the people whom you should want to weigh in on these types of discussions.
It's also worth pointing out that the fact that experienced Stack Exchange moderators and members of the community team weighed in on this discussion does not in any way prevent regular members of the physics site from expressing their own opinions. The engine allows you to post multiple answers to a question for a reason.
Moreover, the concern that someone is going to "take wrong actions against users" on the physics site is misplaced. The only people who have power to take these actions across the entire network are community team members, and they'll have a diamond after their user names even here. These, of course, are "powerful people at superior positions in the overall SE network", although they try not to interfere with individual communities by taking direct action except in cases where it is overtly warranted or where the elected community moderators ask them to step in. However, it is worth noting that moderators on various sites talk to one another. If a user is creating problems on one site in the network, then they are very likely to show up on our radar. There's nothing sinister about that; it's quite clear from all aspects of this site down to the URL itself that it is a member of the Stack Exchange network, and therefore subject to its policies, practices, and community norms.
…a number of people from other SE sites (philosophy, ect) who are not in the slightest interested in physics…
Since you specifically call out philosophy in your question, and I'm a moderator there, I can only assume that I'm one of the protagonists in your tale of abuse. Therefore, I'm not sure where and how you get the idea that I'm "not in the slightest interested in physics", or even the impression that I don't know anything about physics. I haven't shared my qualifications or background with you because I don't think that's relevant. Stack Exchange doesn't have a qualification process for users, it has one for answers—voting. If I were answering physics questions and my answers were wrong, you should downvote them. Likewise, If I'm answering meta questions and my answers are wrong, you should also downvote them. But let's not make assumptions about people you don't know, okay?