You forgot to mention one other domino side effect of this situation: sending Adam Lind back down to the minors... young, cheap and all he needs is the major league experience.
Matt Stairs is a valuable player - veteran presence and leadership, is a professional hitter off the bench, can play 4 positions - DH, 1B, LF, RF. Plus he's Canadian, which is an important bonus for this team.
Reed Johnson was the perfect fourth outfielder - can play all three positions, has some speed, decent defense. But he wasn't a starter for a top team - more of a platoon player/backup - average offensively (no pop) and durability issues.
Shannon Stewart? Noodle-armed left fielder/DH only. Good hitter with no pop. Good base runner with speed. Frequent health issues.
This was a combination money issue and Moneyball issue. Stewart and Stairs platooning should put up much better offensive numbers than Johnson. And you get those two for less than the price of one - even factoring in the almost $550K buyout to RJ. But yikes, the locker room presence, energy and defensive dropoff plus positional flexibility difference is HUGE.
The only other reason I can think of is that Reed Johnson was apparently a bit of a malingerer when he wasn't playing and it's not like the Jays have won anything with him on the roster, you know?
(It's still a head-scratcher. And I hope RJ goes to the Mets and does well for a winner.)