With all respect to rotoworld, I think they're jumping the gun here. While that difference in runs scored looks dramatic, keep in mind that the humidor has been used for less than 20 games.
Even yearly runs scored data for parks fluctuates wildly - Coors included; to truly analyze changing park effects, examining stats by decade makes more sense. Any effect observed in less than 20 games is far more likely due to the way individual players are performing than anything done with the ball. I think rotoworld's statement that the trend will probably continue is premature, to say the least, and isn't dealing with the statistics prperly. In a way, it's similar to saying Cameron will lead the majors in home runs after his 4 hr game. I certainly wouldn't endorse Rockies pitchers any more than I would have befor elearning of the humidor, although Thomson has shown some excellent stuff.
As to the possibility of pitcher injury, I don't see the humidor having any effect - a humidified ball will only make things easier on pitchers by allowing them a better grip. This should also be the primary effect of the "new" balls, with weight differences being negligible.
EugeneStyles raises a great point, though: could it be that Rockies pitchers in general might be more injury-prone, since they'll be subtly changing their deliveries all year, depending on whether they're at Coors or on the road? I haven't seen any stats here, and it may be too early to tell, but this also sounds like a possible explanation of why some Rockies pitchers perform badly on the road as well as at Coors: too many delivery modifications.