[americanSoul]

Shoot him in the knees? Yeah, okay, and while I'm at it, I'll shoot the fly off of his ear.

Exactamundo.

What should the deputy have done, use a knife himself so the confrontation would be "fair"?

You charge a police officer with deadly weapons, expect to be shot in the centre of mass, most probably repeatedly.

[GrandEagle]

Yep!
This one is bad all the way around. No winners.
The guy was disturbed - he really wasn't a nut or anything like that - just very depressed. He had decided to commit suicide and used the poor officer to do it.
The officer came trying to help. Probably excited that he may be able to help this man once again. He tried to get away and couldn't and ended up killing the guy he wanted to help.
He will probably never get over it.
My friend (his twin sister) and his immediate family saw it all unfold. They know that the officer had no choice, but keep playing the "what if we had just ...." game over and over in their head. They will never get over it.

[HELLRAISER II]

I agree and I don't care if the guy's retarded or not. You charge a cop with knives, you take your life into your own hands. He made a decision and it was a bad one, just one less dumb@ss for us to have to deal with.