Mark, if I were you I would dig out all the rotted wood with a Dremel tool or chisels. You need to get back down to firm wood and get rid of ALL the rotted wood. Then you can fill with Bondo if this is still a small hole. Paint will not offer any long term protection. The Bondo will be stronger than the parent wood--if this remains a small hole. If you find that the rot area keeps getting bigger and bigger AND BIGGER as you go, it may be time to call in a pro that can jack the weight off the beam while he replaces as much wood as is necessary.