Manager might also have been trying to show confidence in Sosa. He is a better hitter than he has shown this year. I don't think Thomson likes to bury guys on the bench as much as Girardi did. They want Sosa to get 2-3 starts a week and pinch hit against some LHP. If Stubbs had not hit the previous HR against the guy this move would have not been questioned. Sosa against LHP is probably a better hitter long term than Stubbs is. He just has not been this season for whatever reason (much of it SSS for both Stubbs and Sosa).
Had the situation been reversed and Thomson had put Stubbs in that spot based on a one-AB recency bias sample nobody would have liked that either.
And now it'll be a three-person bench in NY most likely, perhaps with Schwarber available though.
It looked like Schwarber could do his Kirk Gibson impression in the right situation.