I personally do not like meddling with someone else's territory and understand you anger, but Taliban and Al Qaeda seem to have become a global problem which is further complicated due to your limited border precautions and porous regions along Afghanistan Pakistan border.
Hence it leaves NATO little choice but to ask your permission to strike with special forces into your territory.
There are a number of problems with the above. First, is the insurgency problem in Afghanistan localized to the border areas with Pakistan? No. Second, has NATO been able to control the Afghan insurgency in all areas other than the ones that border Pakistan? No, in fact the insurgency has spread far and wide in Afghanistan. Third, is the character of the insurgency in Afghanistan a "hit and run" campaign, where the only attacks occurring are originating from FATA as quick pin pricks by attackers who drive back to NWA before NATO can respond? No.
In other words, do we have ANY reason to believe that while NATO has been entirely unsuccessful in quelling the insurgency in Afghanistan, specifically even in those areas which are far removed from the FATA border, that they would suddenly succeed in FATA? I think in all fairness, the answer is ABSOLUTELY NOT.
So before we start chest thumping with one party saying they will invade FATA and the other saying invaders will be made an example of, let's pause and think about the above. NATO has demonstrated that it is incapable of fighting the insurgency in Afghanistan thus far. On the other hand, the only professional military involved in the wider area which has made considerable progress has been the Pakistan Army. And this progress has been achieved through different tactics and strategy as compared to what NATO has been pursuing.
So, why should we rely on an incompetent, failed force to solve our problem when we have a successful force like the PA already on the ground?
The issue boils down to one of timing and impatience. NATO has to make a withdrawal in a short period of time and now there is a lot of political pressure on leaving under circumstances that are not interpreted as a loss. This political pressure will cause bad decisions to be made at a military level unless the military leadership demonstrates tremendous backbone. Luckily, thus far they have not disappointed. The NYT story was publicly and immediately denied very directly by high-ranking NATO leadership.
We are now in the endgame in Afghanistan and various factions within NATO (political and military) will be carrying out an at-times public campaign using the press as an instrument to gain favour for their preferred strategy. As this fractious process unfolds, there are bound to be days on which NATO will seem belligerent towards Pakistan (as viewed via the pages of leading US/European newspapers) and others on which they will seem friendly and helpful. For Pakistanis, this may seem a bit of a roller coaster, but all of it is ultimately immaterial. This "dialog via the front page" process is their attempt to arrive at a non-embarrassing exit from Afghanistan and is an internal NATO problem, not our problem. The only thing we need to do is draw the line we have already drawn. Whether or not NATO decides to cross this line is their decision. Whatever happens afterwards is ours.