I think you need to bake them/boil them or both to kill off any harmful bacteria... I keep thinking about the salmonella outbreak the US is having right now with tomatoes where over 145 ppl have been infected since mid April. If you go to the FDA website you can see the states that havn't been affected and have nothing to worry about. I know NC and SC are in the clear. (On a side note, the cherry/grape tomatoes and the "on the vine" tomatoes aren't related to the outbreaks, so they are safe to eat! If you have Roma or Plum tomatoes in your house DO NOT eat them unless your state is listed on the website!!).
Anyways, back to the apple wood-- I'm sure if you do some research you can find directions for baking, or maybe a member on here knows how?? Its always better to be safe than sorry... especially when it comes to our babies health.