I think they did all they could given he also held a quasi front office job, which I think is also probably the more important replacement hire. Assistant pitching coaches are more fungible (case in point Sal Fasano getting the Angels job along with their D'Arnaud signing). Kaplan probably just wanted to do the one job they couldn't give him, actual major league pitching coach (and Cotham probably didn't care to move upstairs). I'm sure it also helps improve the brand of his privately owned business.
I wouldn't say we have any assistant GMs who do nothing though.I know you are exaggerating, but all the people who carry that title are pretty crucial (and Mattingly's about shed the "Assistant" but I assume his successor won't get that yet). The only real surprise is that Ned Rice is still here, but he's the contract/snumbers guy.
What's actually funny about all of it is Brent Strom is one of the greatest pitching coaches of the last 10 years, and has far more rings and World Series appearances than our guy. He just took the fall for Arizona's year, and was close to retired anyway before he even went to work there.