Perk is one of the tougher guys in the NBA to play against in terms of strength. Yeah, he can't hit a 15-footer, but so be it. Hasheem Thabeet can hit those, as he showed it in college, so we can claim that he's better than Perk as well under this logic.
(Just joking. As far as I've been a fan of his, Hasheem has been tentative even while just walking on the court. That's another matter to discuss, though.)
Injuries shouldn't be taken into account while discussing about a player's peak performance and Perk simply outclasses Stiemsma with his defense alone.
Let's have Stiemsma defending Howard 1-on-1 without getting into foul trouble and then re-evaluate this topic.
On another note, I'm not saying Perk is all-star caliber or something, but could be a starter when healthy, while Stiemsma will never be anything more than a 2nd string center.