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Not denying that as a possibility.  I think, however, that you're oversimplifying the run of good results...I see:
Jackson gets hot in May, runs off a great string of starts...and then his normal command problems return, but the runs don't show up for a while because he's getting lucky on HR/Fly.  Until late in the season.
Look...his first two months he walked 18 guys in 74.1 IP (2.18 BB/9), followed by 52 walks in the remaining 139.2 IP (3.35 BB/9), and no...that's NOT biased by September...his problem that month wasn't the walks.  Check the HR rates for better information on what actually caused the skid: April to June - 7 HR in 108.1 IP (unsustainably lucky)...July-August-September - 20 HR in 105.2 IP (his career HR rate is 82/670, so the 20 is probably a bit UNlucky.
It's a mistake to look for command using only K/BB...you have to look at how poor command can otherwise manifest...HR rate is one major way.  Team-relative BABIP is another (and Jackson had a major return to normal in his BABIP starting in August...he was pitching unsustainbly LUCKY in that regard early in the year but returned to career norms at around .315 in the latter months - his career total is .306...he's been consistently more hittable than his team defenses, it's worth noting...and that comes from...wait for it...POOR COMMAND).
And BTW, whether you like it or not, you position has to do with BOTH Morrow AND Jackson and your evaluation thereof.  You can't decide whether Jackson for Morrow/Kelley is a good swap or not unless you make an evaluation of both pitchers.  You evaluate that Morrow might, some day, be what Jackson was in 2009 and use that as a reason that deal is a no-brainer...because you project that Jackson will return to 2009 value in 2010.  I reject your assertion with the claim that Jackson isn't really as good as his 2009 value, meaning if you expect Morrow to come anywhere near reaching Jackson's 2009 value, you should keep Morrow.  Those are the terms of this debate.