Thanks very much Belinda and Hermann - this was something the school had mentioned but I was under the impression that universities didn't like AS or A2s to be taken early, or to be spread over 3 years.
They don't as a rule, but this is such an odd situation that if the child did this general qualification and then went on to do other Science A levels over the right time span I think it might work. The AS would be finished by the start of sixth form and as it is very general I doubt that universities could hold it against you. Better than doing nothing.
If this were me I would write to the Chair of Governors at the school asking for assurance that science education would continue for Year 11 students, bearing in mind the compulsory nature of the subject through KS4. I would hope that as a parent I wouldn't be put in the position of having to make suggestions, but it sounds like this one is reasonable if you are.