The desert eagle just looks like the kind of gun that could shoot someone's torso off.

Wouldn't it be cool if agent smith dual wielded cz-52s.

The agents were programmed to take the form and mannerism of FBI agents, so despite the holding of Desert Eagles, they are firing with one hand because a computer program could be designed to handle the recoil.

I tend to think that whole excuse (which fans of the movie always use) is kind of a copout, i.e. "The Skorpions can eject .223 casings because it's The Matrix, DUDE!"

In real life of course, the agents can fire Desert Eagles one-handed because they're using low-recoil blanks.