I think you're missing the point. A 5-day suspension means that 5 days worth of a player's salary goes into the player's union's coffers (I believe, maybe it's the MLB coffers). The way a team chooses to use its players has no bearing (and shouldn't) on the manner in which the MLB assigns suspensions.
What if a team used a 4-man or a 3-man rotation? Would you hand out suspensions differently to those teams? What if an AL pitcher was such a good hitter that he DHed on his non-pitching days? Would you fine him differently?
Suspensions are meant to hurt the player (in his pocket) and not the team although that's the result. Some suspensions hurt more than others. Should Todd Pratt have been suspended additional games because he isn't as valuable to the Phillies as Ortiz is to the Red Sox?
It would be impossible to create a "balanced" system.
Maine has a good swing for a pitcher but on anything that moves, he has no chance. And if it's a fastball, it has to be up in the zone. Basically, the pitcher has to hit his bat. - Mike Pelfrey