I was confused about this too, as I'm currently playing a Lawful Good Cleric of Wee Jas. However, I figured it out. Allow me to explain.
If you read it closely, it doesn't say that ALL Clerics of Wee Jas channel negative energy- all good Clerics channel positive energy, and all evil Clerics channel negative energy. The distinction with Wee Jas is for NEUTRAL Clerics. When a Cleric is Neutral, it causes a problem or two, depending on the deity's alignment.
Neutral Clerics of a Good god channel positive energy. Neutral Clerics of an Evil god channel negative energy. Good Clerics of a Neutral god channel positive energy, whereas Evil clerics of a Neutral god channel negative energy. When both the Cleric and the Deity are neutral, however, generally the Cleric can choose which he wants to channel (negative or positive). However, in the cases of St. Cuthbert and Wee Jas, ALL Neutral Clerics of St. Cuthbert channel positive energy, and ALL Neutral Clerics of Wee Jas channel negative energy.
However, the issue in my mind is that the Player's Handbook states that Rebuking Undead is ALWAYS an Evil act, whereas Turning Undead is ALWAYS a Good act. While I believe they can be used for evil or good purposes respectively, that means nothing in terms of good acts and bad acts. Turning can be used for Evil purposes, and Rebuking can be used for Good purposes- thus, Turning and Rebuking are no more inherently good or evil than wielding a sword. But that's a whole different story altogether.