The extremists in Pakistan were condoned by Musharaf. When he lost power a moderate government came into power, but they do not have much control over the extremists yet. They do not protect them as much as Musharaf did though.
India and Pakistan have always had 'strong arguments', but the current Pakistani government is more willing to help India than the extremists in this situation.
The extremists responsible for these attacks (whether from Pakistan or the border region of India) wanted to provoke an aggressive response from the Hindu extremists, as the people who would fall victim to that would be normal citizens and this would be a powerful recruiting tool for the extremists again.
Now back to the original question: The 'War on Terror'. The Pakistani government does not want a bloodbath, and is willing to help India hunt for those responsible. If India keeps on claiming Pakistan is responsible and wants to attack Pakistan you'll probably get a nuclear war in the region. Pakistan knows threatening won't keep those wanting a war at bay, so while talking with the part of the Indian government which wants peace they want the US to keep those that want war at bay.