Yeah, Jordan's comments were damage control, really. But I don't think Brundage realized the extent to which that drama would travel beyond the Lehigh Valley media. Mackanin is a little bit that way too, not realizing that in this day and age his postgame comments won't be buried in the paper the next morning, but will rocket around social media and CSN Philly with the same weight as any other story.
I don't think Brundage was wrong to do what he did though, and thus far it sounds like Williams took the lesson.
It's really hard to be a Phillies prospect right now, not only do you have the usual orneriness of the fan base, but you are both in the shadow of the '08 group and in an organization that literally doesn't have a single star ("star" being defined in this case as someone who might finish Top 10 MVP or CY). These OFs all have a chance to be really good major league players but there's gonna be more Marlon Byrds than Jayson Werths (and a few Dom Browns). Franco is already in that boat to some extent and Crawford will be too, the hype raises expectations and everyone loves a breakout rookie, but good players who take a few years to become great are more common.
It's not like Klentak doesn't know all this though, that's why he has kept so many options open, isn't rushing prospects and is primed to sign a FA OF (or trade for one) next year if necessary.