Much like the situation with Thomas, this seems like it is punishing a team for something beyond its control. I wonder if there will be some attempt to modify this in the next CBA?
A couple of thoughts:
If a player has already missed an entire season, he can be placed on a list for subsequent seasons. Players on this list would not have their cap hits count towards the teams cap for each season on the list, but he must remain out that entire season.
A more aggressive addendum to this: If a player's injury is the result of a suspension-worthy play, the injured player's cap hit for missed time (probably offset by a year) would be transferred to the suspended player's team (this would stay with the team, not transfer with the player).
Are this modifications that would seem worthwhile?