The deals given to Eddie would be unlikely, as a homicide charge would trump a sexual battery charge. Additionally, the gun would have been checked against records and would have turned up as missing from the federal operation, so there was no need to make a deal regarding the ATF agent.
Stabler tells Eddie the bullet that came from his gun is on the left and the one that killed Annete is on the right and shows him photos. The photos are of firing pin impressions on shell casings, not bullets. It had already been established that the bullet that killed Annette was unusable due to kitting a wall.