I'd go for wooden spoons over plastic ones any day. Especially since the wooden ones don't melt
Also, bacteria (in your wooden spoon or from your cooking board) won't survive any temperature at which you cook your food anyway - so I wouldn't worry about that so much.
Besides, a few bacteria won't kill you instantly, as HentaiKid said. If you wash your wooden cutting boards after use I can't see any problems. Well, never had any problems at any rate.