Nice catch but i'm fairly certain that ISI is fully aware of all such locations in the country.
The problem isn't that they don't want to take these madrassas on, the problem is that they are calculating the backlash that will arise from such operations. Think of how many people, to this day, believe whatever Mushy and Army did in Lal Masjid was wrong.
My feeling is that ops against such madrassas are lower in the list for the time being. Top 3 would be wrapping up Zarb-e-azab, Karachi OP and whatever the hell is happening in Balochistan.
But some day one will have to face the reality and deal with it, one way or the other. If the authorities are aware and doing nothing about it, then it is even more alarming.
It will grow only bigger and bigger with time and more difficult to handle later.