Given that the 22-yo Milton man did actually kill the intruder, obviously he must be charged with, and convicted of, 2nd degree murder (i.e at the moment he pulled the trigger, he intended to kill the intruder -- but it was not premeditated.)
Except that The Criminal Code of Canada says:
Section 34 – Self Defence
34. (1) A person is not guilty of an offence if
(a) they believe on reasonable grounds that force is being used against them or another person or that a threat of force is being made against them or another person;
So, if the police do indeed fully accept that it was self-defence, it is proper for the police or prosecutors not to lay the charges. However, if the police have even a slight doubt that the self-defence is dodgy, they should press the charge of murder-2 (which is already admitted, in this case) and let the court decide on whether or not the self-defence removes the guilt.