That's the main issue, I think. Giles and Monty were the CEOs, with an ownership stake. They hired the GMs, signed off on the biggest decisions, and were empowered to act on behalf of ownership, and also represent their underlings (mostly the GM but also marketing) to ownership. In theory that is also MacPhail's job, but Middleton is doing it himself.
If MacPhail was the one actually doing Klentak's job for him, that would be more justifiable. Friedman is running the Dodgers without a GM right now. The baseball bosses in Chicago and Minnesota are obviously in charge over their GMs. But MacPhail doesn't seem to be a hands-on baseball guy either.
I tend to think meddling owners are always bad, but at the same time, meddling owners often (though not always) correlate with championships. Probably that is also because meddling owners also correlate with high-payroll teams. Best case is Steinbrenner, Mark Cuban, the current Red Sox group. Worst case is Ed Snider (though he wasn't so bad before there was a salary cap) or Jim Dolan.
I think the more subtle problem is that owners only react to the big money, obvious stuff. Like Bryce Harper or Gabe Kapler. Neither Middleton nor MacPhail were qualified to hire the scouting director, or to hire last year's new development director. They still believe in Klentak enough to leave that to him, and also to leave the entire coaching staff in place, so we'll see what this next move does to the mix. If the new manager, pitching coach and hitting coach don't believe in the philosophies that are being instituted by the GM, development director and scouting director, how's that work exactly?