I am typically loathe to second guess a fellow LEO's actions, but there are only a few reasons that I could see for going into a closed trunk to get a pistol:
1) to verify that the firearm is actually in the trunk, not under the driver's seat. This can be done visually, however.
2) to ensure that the weapon is not a prohibited or illegally owned one (is it the .38 she said it was or is it a full auto Mac-10?). Generally this can also be done visually, but in states (like mine) requiring a permit for a handgun the LEO may need to handle the weapon to check it's serial number.
3) if it is illegal in that state to transport a loaded weapon. In this case the LEO may have to handle the weapon to unload it but, if he/she is unfamiliar with the weapon, it is not immediately necessary and can wait until someone with more familiarity arrives on scene.
4) the "trunk" is actually a hatchback, or can be accessed by the occupants of the vehicle. In this case, it is a judgment call to remove the weapon or remove the occupants. Both have pros and cons and either is tactically acceptable based on the LEO's knowledge of his own strengths/capabilities.
In MY opinion, based on professional experience but few details on this specific incident, a weapon in a trunk is not an immediate threat. Unless a visual inspection proves it to be an illegal weapon or circumstances lead you to believe it is stolen, handling the weapon appears to be unnecessary. Short of the 'cocked, loaded revolver loose in the trunk and snagging on something' scenario, I don't see how a weapon that was handled safely would AD and strike him in the leg. I am glad that no one was killed, and hope that this motivates this Department's firearms training instructor to start reviewing the BASICS of safe firearm handling, stress that these principles apply OUTSIDE of the range, and go over the proper unloading of a variety of common weapons--many officers, especially those in non-gun states, have had no exposure to different weapon systems beyond the one they carry. It is foolish to ASSUME that someone with no prior weapons exposure would instinctively know how to unload a revolver when the only thing they've ever touched is a semi-auto.
As far as all LEOs being highly trained weapons users...sadly I have to concur that I've seen some of my brethren do STUPID things with a gun (just as I've seen potentially fatal things done by civilians at the range). I've also seen plumbers that set fire to homes while soldering pipes, mechanics that "forgot" to put brake fluid or oil back in the car they were working on, and other people who have done their jobs poorly due to stupidity, carelessness or lack of training. Unfortunately, when that person is an LEO, the papers are quick to jump on the story and people (even some of the people here) are equally quick to jump on the "let's bash LEOs" bandwagon.