From what I'm seeing, Jons major problem (and this will follow him in the majors for as long as he's here) is his seeming unability to get a single strikeout. Once in a while, in situations like this one, a K is HUGE, and he's unable to get ANY. He needs to either begin working on some sort of cut fastball or slider so he has a strikeout pitch he can toss from time to time.
In the majors, even the slowest of pitchers like Maddux get strikeouts, situations like one Jon is in now make them absolutely necessary.
-y2