I recently ran across this interesting article about using a sous vide to make safe-to-eat raw cookie dough.
According to the article, flour needs to be brought to 160 F to make it safe for raw consumption. She uses her sous vide to do this though admits it takes a really long time for the flour to come to temperature (four hours). She links to another article that was able to do the same thing in a 1200 watt microwave in 55 seconds... which gives us another option for home flour pasteurization.
As pointed out in the second article:
Heating flour to this temperature runs the risk of burning the flour, therefore heating must be done carefully to ensure flour does not get too hot and burn. Also, heating the flour to 160 degrees F destroys some of the gluten in the flour and therefore would make the flour no good for baking. However, the flour is still useful for creating treats that will not need to be baked.
So, if you want flour that can be used in unbaked products (cookie dough), both the sous vide and microwave are options.