It may not be a problem that needs to be dealt with. There are successful pros (e.g. Glavine) who do this.
But can it lead to injury? I believe so for two reasons. First, it directs the arm closer to the end of the shoulder's range of motion in the throwing direction. Second, it can limit hip rotation which means the pitcher might not be able to use his body as well and end up throwing with more arm.
One solution you can try is to look at his drag line and move him to the one side or the other so that his drag line ends on the centerline between the pitching rubber and home plate. So for your lefty, if he strides to the left (and his drag line goes to the left as well), have him start on the right side of the rubber. This reduces how big of a corner he must turn to get squared up to the rubber and, therefore, how much he throws across his body.