Well to be fair, he was given information that the typhoon would pass the Third Fleet and he took the chance of not cancelling already planned operations. As taken from Wikipedia:

"In fairness, he received conflicting information from Pearl Harbor and his own staff. The Hawaiian weathermen predicted a northerly path for the storm, which would have cleared Task Force 38 by some two hundred miles. Eventually his own staff provided a prediction regarding the direction of the storm that was far closer to the mark with a westerly direction. However, Halsey played the odds, declining to cancel planned operations and requiring the ships of Third Fleet to hold formation. On the evening of December 17 the combat air patrol over Third Fleet was unable to land their aircraft aboard the pitching and rolling carriers. The pilots were forced to ditch in the ocean. The aircraft were lost but all the pilots were picked up by escorting destroyers. By 10:00 am the next morning the barometer on the flagship was noted to be dropping precipitously. Still the fleet attempted to maintain stations. Finally, at 11:49 a.m., Halsey issued the order for the ships of the fleet to take the most comfortable course available to them, something which many ships had already been forced to do. Between 11:00 a.m. and 2:00 p.m., the typhoon did its worst damage, tossing the ships in seventy-foot waves. The barometer continued to drop and the wind roared at eighty-three knots with gusts well over 100 knots. At 1:45 p.m. Halsey issued a typhoon warning to Fleet Weather Central. By this time the Third Fleet had already lost three destroyers. The storm inflicted damage on a great many ships in the fleet, with the loss of some 802 men and 146 aircraft. Third Fleet conducted search and rescue operations for three days following the storm, finally retiring for repairs at Ulithi on December 22"