Perhaps once he is older, and almost certainly after he has become a Servant and learns of the existence of Second Magic--the thing that is used to explain alternative timelines in his world--Diarmuid will understand. He will understand and argue with September that there must be another way--another way that doesn't involved erasing the good with the bad.

However, for now, it is for the best that September doesn't try to explain. Diarmuid will just be confused and perhaps even scared. After all, he likes September and the last thing he wants is for the man to cease to be.

"I am sure he will do very well too! He has you to look up to even if you can't be with him. That means he will be kind and smart and strong!"