I agree stats can hide issues in the minors. Not saying command wasn't an issue before, but I've never really seen BB/9 jump that much, almost double, simply because of going up a level, Even going from AAA to MLB it most often doesn't jump that much.
The tacked baseball could be part of the issue, but that's totally different than players in AAA having better plate discipline than AA and below. Maybe his BB/9 rate won't fall back to around 3.00 consistently but it's hard to believe he'll stay up around 6. If he can manage around 4 he should be ok.