I don't know how I'd feel about getting him out of his chair, I think that would be kind of like the bad old days of how we used to never photograph disabled people in a wheelchair. The wheelchair isn't the problem.
From what I can see, it seems that you could have easily just shuffled the students over towered the wheelchair, and moved him in a bit closer. There would be a little bit of bench sticking out, but it's better than this solution to have the kid leaning in as if to say "hey, i'm over here! I want to be part of the group, but I just can't because of this chair!"
But taking the chair out of the equation is not the solution IMO.
The article states that they, the care staff, are able to take him out of his chair for the school photo like they did for the second image. Therefore, no extra attention is placed on him in the school image at all. Problem solved. He can be just like his peers. Just because he needs a chair most of the time doesn't mean it needs to be documented as such.
Historically, though, this is kind of politically incorrect. Though out the 19th and early 20th century, wheel chairs were such an object of shame or even disgust that they were never to be seen in photographs, and great lengths would be made to prevent them being seen at public functions. In fact, it was frequent that the chair-bound to not be encouraged to participate in outdoor actives where they could be seen in their chair.
While relocating him from his chair might be a good option for this individual and this family, I don't think it is generally a good way to handle the situation due to the historic implications.
Being a person with a psycho-neurological condition, it is very easy to hide my disability. But I don't think that hiding disabilities is an acceptable approach to fighting stigma, and popular acceptance must come disabled or not, chair or no chair.