How I would have concluded this fim.

I would have the guns collected from the hospital siege tested for ballistics as a standard procedure.

I would have the prostitute's gun (the cop killer) identified during these tests.

I would have the lab gun tester tell Murphy about the gun before anybody else.

I would have Murphy tell the lab guy to keep this news between them and have Murphy leave the lab with the gun which killed the cop killer.

Finally I would have Murphy gun down Morgan, the cop who threw the kid from the roof.

It will be assumed the cop killer got Morgan when the slugs in his corpse are found to match those from the gun which killed the rookies at the start.