Voldemort didn't know.
"Here is the thing: for convenience, I had Dumbledore say to Harry, "You were the Horcrux he never meant to make," but I think, by definition, a Horcrux has to be made intentionally. So because Voldemort never went through the grotesque process that I imagine creates a Horcrux with Harry, (SU: Mm-hm.) it was just that he had destabilized his soul so much that it split when he was hit by the backfiring curse. And so this part of it flies off, and attaches to the only living thing in the room. A part of it flees in the very-close-to-death limbo state that Voldemort then goes on and exists in. I suppose it's very close to being a Horcrux, but Harry did not become an evil object. He didn't have curses upon him that the other Horcruxes had. He himself was not contaminated by carrying this bit of parasitic soul." — [Pottercast 12.23.07 - The Leaky Cauldron][1]Pottercast 12.23.07 - The Leaky Cauldron
Harry was not deliberately made into a horcrux, so Voldemort had no reason to avoid killing him. [1]: http://www.the-leaky-cauldron.org/2007/12/23/transcript-of-part-1-of-pottercast-s-jk-rowling-interview