Injuries aren't such a big deal in this instance, since the WC is still 8 months away. The bigger issue is taking players away from their club teams. It's especially painful for MLS teams like the LA Galaxy who are making a playoff push and have to go without two of their best players (Landon Donovan and Omar Gonzalez) for yet another stretch at a crucial time for them. (Actually, the Galaxy will miss their three best players because Robbie Keane also takes off to play WC qualifying games for his home country, Ireland).
Yes, players can get cold. It's hard in soccer to coordinate having your players peak at the right time because the international schedules are so crazy. The World Cup is in June, when the European leagues have just finished their long seasons. As a result, these European-based players are definitely "in form" at that time, but they may also be exhausted. Conversely, the MLS season runs in the summer through the fall, so the World Cup comes at kind of a down time for them. They try to stay fit with international friendlies and occasionally playing "on loan" for a while in a European pro league to keep their fitness and sharpness up. The timing is tricky with these things.
Edit: In this case, for the U.S. qualifying games, they are still pretty much playing their A squad, with some fringe players mixed in. This is because they are still trying to build team cohesion and because they have to determine exactly who needs to fill what roles.