The part i'm unsure of is the effect of a real operation might have on me,
Im not sure exactly what you mean. Going on operation is certainly not going to impede your flying career in anyway. Guys with operational experience are what the airforce need.
but what if i'm sent on an operation and the affect seriously impede on my ability to go on in the air force?
It sounds a bit like you wanna join the RAAF to fly, but not to go to war. You are signing up to 12 years of serving your country. If that means flying in dangerous areas, so be it.