The scapular loading and catching up in Crow's arm motion are red flags, but not necessarily problems. I am not convinced that injuries are in his future, but if they were to appear I would have a good idea why. I have read into both sides of the argument quite extensively and tend to think that neither side has an argument that blows the other out of the water.
Lincecum has unorthodox mechanics and by no means would they work for the majority of pitchers in the majors, because they are tailored to his body type and what his ligaments can withstand. Most people who have written on the subject of Lincecum's mechanics will frequently point to his athleticism as the lynchpin to his success and injury free history (thus far). The good news is that Crow, too, has been cited for his athleticism and it is possible that this could be the major factor in preventing possible injury to his body.
But to say Crow is not at risk is not valid. The timing in his windup causes his arm to catch up before the point of release, putting an unneeded amount of stress on his rotator cuff and possibly his elbow. A good example of guy in our system with the same arm motion is Atilano, who saw his season come to an end in 2006 because of elbow issues. The motion Crow has now works for him, so I wouldn't suggest changing it, especially the risk that comes with messing with a first round picks mechanics (see Detwiler). While there are these red flags, Crow has some excellent "stuff" and I don't think you let him walk because of possible injuries 3 or 4 years down the road.