Although there is a correlation between conditioning level and certain injuries, I don't believe for a second that the cataclysmic injuries of the last two seasons (Harrell, Inky, and Jason Allen) can be attributed to that.
Inky's injury was literally a one-in-a-million occurrance, although the way most guys tackle nowadays (lowering the head and shoulder rather than squaring up and locking on) I'm surprised it hasn't happened before. The so-called shoulder stingers are basically slight versions of what Inky suffered, which could have cost him his arm above the shoulder.
Jason Allen suffered a hip dislocation, which is nearly impossible to do under any circumstances. In the case of the shoulder, the stronger the muscle is around it, the less likely a dislocation will be (although it only reduces the risk to a point). With the hip, there's nothing that can be done to reduce that risk except for the fact that even dislocating the hip of a cadaver is nearly impossible, even using power tools. That should give you an idea of how rare that injury is.
I think the reason those injuries hurt more than in prior years is because the depth simply has not been there. When Jamal Lewis got injured, for example, Travis Henry and Travis Stephens stepped up. When Al Wilson was hurt, Chris Ramseur was an adequate stopgap. When Billy Ratliff was injured, he was replaced by any of Ron Green, Jeff Coleman, Fred Weary, or Darwin Walker. But the last few years have been worse because of the lack of adequate depth.