As some of you may know most ford 9" axles don't come with a drain plug and you either have to pull the third member or try and cram a hose down the fill plug to suck out the oil.

My question is this: can I drill and tap a drain plug hole without pulling the axle apart, just carefully drill the hole, wait for all of the oil to drain out and tap and screw in a plug?

You could do it that way, but IMO having a drain plug on the bottom of the diff is a bad idea. You do enough scraping over rocks and your going to mangle that plug and make it so you can't get it out. Or worse, deform the area around the plug so it leaks.

There are a couple other options:
Pull the third, knock out the bottom stud, then tap the hole and replace the stud with a bolt. Then you can remove the bolt when you want to drain. It's slow, but it's cheap and it works.

Another option is to pull the third and install a weld-in fill bung on the back cover. Then you can put a hose in it and drain it.

http://www.ballisticfabrication.com/Weld-in-fill-plug_p_1593.html
http://eastcoastgearsupply.com/i-134309-differential-fill-inspection-plug-kit.html

I was thinking about offsetting the drain plug to the side a little way ( like a toyota drain plug), the truck in question is my farm truck/ light duty tow rig/ light off roader so trail damage is not a high concern. I was more concerned with interference with the plug inside the axle and the slight possibility of a few metal shavings from the drilling and tapping process remaining inside the axle.

I don't think the housing is going to be thick enough to securely hold a drain plug. The material is around .125" thick, which even with a fine thread there wouldn't be enough threads. I think the best thing to do would be to go ahead and pull the third this time and remove the bottom stud as I mentioned before. The material at that mating surface is doubled and would have plenty room for threads.

I welded a piece of .25" thick plate to the bottom of the housing and ground the corners down so there isn't anything to grab on a rock. Then drilled and tapped for an allen head plug that recesses in maybe .03" below the surface of the plate. It works good so far.