Yes, the US should stop helping Al-Qaeda, even if we think they are pursuing our interests in some parts of the world. Al-Qaeda is using the tools that the United States is giving them, and even our weapons, and they are turning those skills against us, like they did on September 11.
Yes, if the US is indeed helping Al-Qaeda in any way, it should stop. Helping a terrorist organization is a terrible thing to do, especially when that terrorist organization has carried out attacks on your own homeland. Thus, if the US is helping Al-Qaeda in any way, it should stop.