He has remembered that he is dreaming, and is asking Cobb if he has come to awaken him from that dream.
Look at what immediately follows that line; Saito takes Cobb's totem and states that he knows what it is, indicating that he is (now) aware that he is within a dream. Given that the film previously established that dying in a dream will, under normal circumstances, awaken the dreamer, he is most likely using the phrase "kill me" to mean "awaken me". (Being "killed" is how Ariadne and Fischer are explicitly shown to have exited from Limbo, at which point Cobb had refused to let Ariadne kill him until he had found Saito.)
Additionally, it didn't make it into this scene in the film, but the script had Saito pass the gun to Cobb prior to asking that question. Hardly an action he would have taken had he thought Cobb was an assassin.
The Elderly Man watches the Bearded Man WOLF down his food.
He SLIDES the handgun down the table towards him.
ELDERLY JAPANESE MAN (in English)
Are you here to kill me?
The Bearded Man glances up at him, then back to his food.
The Elderly Japanese Man picks up the cone between thumb and
forefinger.
ELDERLY JAPANESE MAN
I know what this is.
He SPINS it onto a table- it CIRCLES gracefully across the
polished ebony... a SPINNING TOP.
ELDERLY JAPANESE MAN
I’ve seen one before. Many, many years ago...
The Elderly Japanese Man STARES at the top mesmerized.
ELDERLY JAPANESE MAN
It belonged to a man I met in a half-remembered dream...
MOVE IN on the GRACEFULLY SPINNING TOP...