Stray cat attacks my cat?

I have 2 cats I used to have 3 but the last time I saw the 3rd cat. The stray was attacking him I ran outside to stop him but they both ran off I haven't seen him since I am convinced the stray scared him off for good. The problem I have is that he is not only a stray but he is the father of my boy cat too I have a female who after she had 2 litters enough was enough I had to get her done but I kept the 2 boys from her first litter as I said before I only have one now, at the moment am torn if I don't lock the cat flap at night he comes in the house but he doesn't just eat and go he comes upstairs when we are sleeping and attacks my boy cat I have never seen him attack the female I think its a territory issue, I haven't got my boy done yet because am scared that it may tame him enough not to be able to protect himself and to be honest he's not much of a fighter as it is, he's friendly homely and prefers to be in the house with me, he follows me almost all the time but what can I do when he's not even safe in the house I don't want this stray to drive him off too. Has anyone got any advice.