I'm not sure we can plausibly argue that it was an obvious mistake to keep Rupp and Galvis when neither of their ostensible replacements look ready in AAA. That's not to say Knapp and Hanigan (or Ellis) wouldn't have been fine. Heck, Andres Blanco at SS would be fine. And if the Phillies actually need Rupp and Galvis in 2018 they have bigger problems. But it's not out of the question.
I think Klentak has plenty of autonomy, and I also think the process is a lot more collaborative than we like to imagine (and that was also true before). If it's true that ownership, above MacPhail, decided they wanted to add payroll and have a more respectable team, more Giles-like deals wouldn't have achieved that, or sold the team as being worth a look this year. That may not have been Klentak's choice. But nobody expected the pitching to be this bad, or the two players you could write down in ink to struggle.