Parents will sometimes argue "My child is extremely bright, hardworking and well-behaved, so there'd hardly be any prejudice at all!
" - but I think this approach is unlikely to work. Prejudice is invariably looked at in general terms - not in terms of the degree of prejudice caused by the individual child (apologies if that's not what you have in mind).
In my view, it is quite clear in the Code that it is the parent's reasons for wanting a place at the school that are being balanced against the school's case for prejudice.
Overall ability might just fit if this is the only school around that could meet your son's academic needs and enable him to reach his full potential. If there are other grammar schools that are accessible, though, it's unlikely to be much of an argument for this particular school.
If the school is noted for its strength in a particular subject, and this is something that your son excels at, then that could be a good point to make.