That sounds very hard, but it might be doable. I've seen 3D characters in stages, and I've seen near-fully flexible animation, so...
But the guards themselves shouldn't shoot you too often or too effectively.
It's not like they are the ones you're fighting, anyway.
Imagine fighting on top of the catwalk, then one of the guards see you, he then fires a few shots and runs away, and you can hear him call up on his radio, calling for backup. Suddenly you hear the sirens, then guards pour up to the catwalk, fire notstop and shooting anyone they see. If you drop down to the ground, the guards will toss and throw grenades over the side, or send a few guards to the ground to attack. If they can't find you anymore, or if you have defeated a certain number, the guards will leave.
The only problem is that the stage would be so hard to fight on due to the guards.
Then again, that would be so awesome.
If that is somehow possible, we should make a version with and without guards.
That is, and probably is impossible.