There are many pilots who pray while taking rest and No they dont have to pray in the toilet! no one can force anyone to pray in the toilet. Sure lightning wont strike, if a prayer is missed. I dont know what type of culture is there in CX. I am sure any pilot who wants to pray would himself make sure to pray out of Pax sight.
The only problem I have is why if CX is going to Pakistan, and suddenly someone mentioned how a pax would react seeing a pilot praying in the business class. It only shows lack of tolerance. I am not going further into this discussion, You guys carry on with your routine discussions.