How do you propose "protecting" Pakistan's nukes? Do we invade Pakistan and take charge of their nukes? Do we wait for Pakistan to be on the brink of collapse and then step in?

Your historical analogies are not relevant to today's environment. This is not like the British Empire or Russia trying to take control of Afghanistan where it is the entire Afghan people against an invading force. The Taliban are now just a minority rebel force against both the majority Afghan population as well as a coalition of forces that are there to help the Afghan people maintain their freedoms that they did not have while under Taliban control. The Taliban are a much smaller force, without the level of funding and support, than the mujahadeen that faced the Russians. Hence, to assume that they can not be defeated based on historical precedence is inaccurate.

I also disagree that the threat of a Pakistan bomb is only with a war with India. If Pakistan were to fall to the Taliban, there is no limit to the imagination as to what they might do with a nuke or allow al Qaeda to do with one.