They guy cutting his hand with the knife was the guy Smith overwrote in the matrix. He is effectively now a Smith too.
About all the weird sex stuff. Apparently Larry Wazkowlski, one of the writer directors is currently having an affair a bondage Mistress. His wife was heard to comment that she wouldnt have been surprised if he was wearing a bra and panties under his suit at the premier. I guess that explains any sexual oddness. Be nice if he left his freakoid fantasies out of the movie, I dont care what way he swings but they could have used that 5 minutes for a cool action sequence.