It remains to be seen about Kapler. I think his public relations capital (and Klentak's capital) is dwindling. If they finish decently and over .500 he is probably fine but if they have a losing record in June, July, August and September, they won't finish over .500.
And Klentak will also have to think about his own job. If he keeps Kapler and they fail next year he might not get to hire the next manager. If he hires a new manager this year he's probably good for two seasons.
To me the wild card is MacPhail and Middleton. This Mallee move seems like something that probably came from them. If Middleton is unhappy with Klentak (and we don't know that he is) that ultimately falls on MacPhail. Pure speculation but this just feels like something where Klentak and Kapler have repeatedly defended Mallee and said changing the hitting coach wouldn't make a difference (which it likely won't) until one day Middleton just decided he was tired of watching this offense, demanded change, and installed an old-timer whom he's known and loved for a lot longer than his GM or president.
As for who hires the coaches I think Kapler makes the final call but Klentak has a ton of input, which is pretty much how it's always done. In this case they were probably perfectly aligned (originally I mean. Maybe not now!)