Sorry about your situation but I wouldn't panic.
I did triple science at GCSE level, doing French, History, Geography, Business, top set English and middle set maths. I now do Biology, Chemistry, Economics and English. I know many people who got the same results as me in year 9 and got turned down. It's not just about grades, its about how the pupil deals with lessons as well as their other subjects. If they are doing conflicting lessons they can't do it (eg timetables over run), and often if the subjects are heavy in coursework or rated as quite high tear (which histroy and french are) they could get turned down. After all, they are fitting another module in in the same time as others are doing the normal amount.
I wouldn't worry too much. Employers, uni's and sixth form don't look at what type of science you take so long as he does well it shouldn't matter. The entry requirements for most science A-levels require a B in that subject, you do not need to do triple in order to do them. Also, I'm not doing too well in one of my sciences, and yet I got straight A's at GCSE, so I know as well as anyone that they are no representation of GCSE's and are completely different. :)
Let your son know this, he shouldn't be down about it because so long as he aims for B's (and he clearly has the ability to get A's and A*'s) he'll look equally as impressive as a stressed triple sciencer trying to finish their course! :)