Remember that English is also an official Language for the Maltese Islands so legally they can't ask for Maltese only!
Further more if one lives in another EU country such as Germany,Italy or France where there are no GCSE exams but rather Abitur,Matura and Bacc. they are direct equivalets of GCSE's.
All you have to do is ask your country's Education department for an equivalency Certificate!
If Airmalta don't accept this they are breaking EU regulation on mutual recognition one can lodge an official complaint with the EU commision per email and they will take action.