There is no real short-term fix to deal with these people. They are a result of a whole decade of radicalization in the 80s. What needs to be done though is:
1.) Media ban on ALL mullahs/preachers EXCEPT those that are authorised by the state.
2.) All jummah khutbas to be issued by the state, one jummah khutbah to be read all across Pakistan. Of course, we have many sects in Pakistan, so khutbah should carry the same message BUT should be flavoured slightly differently for Shia and Sunni mosques.
3.) Mosques, madrassahs, and seminaries ALL under state control/supervision. Curriculum, khutbas contents, etc should all go through checks for extreme content by the state. No mosque should be allowed to recieve foreign funding, this is to prevente exremist Islam, and political Islam, such as Saudi wahabbi ideologies and "Khamenei/Iran worshipping" wilayatul faqih Shia ideologies, from entering Pakistan.
4.) Establish Sunni and Shia seminaries across Pakistan which will issue qualifications to become a Maulana. No one should be allowed to preach without a valid qualification from a recognized seminary.
5.) Arrest all those who protest violently. Change jails from being punishment focused, to being rehabilitation focused. Prisoners should be educated with basic literacy requirements, Islam (if they are Muslim), and should also recieve some sort of professional training. They should also be assisted in finding work upon their release.
6.) ALL kids need to go to school, there should be no kids out of school. Pakistan must make 100% literacy a top priority. Madrassahs need to be mainstreamed to teach regular subjects, and all Islamic curriculum should be controlled by the state.
7.) Establish technical colleges across Pakistan to give people skilled training. This should be marketed as a viable alternative to traditional universities and should be targetted at the lower class.
8.) Create jobs across Pakistan so that there are less unemployed people, and hence, fewer people sitting around all day and thinking too much for their own good.
9.) ISI need to carry out a massive operation to infiltrate all these groups such as TLP, MMA, etc, create discontent, and bring down their top leadership one by one. Destroy them from within, expose them, turn them into a disgrace in the eyes of the public.
10.) Council of Islamic Ideology needs to be useful now, and start promoting a moderate Islam to counter the TLP and extremist agenda. The recent campaign for women's inheritance was a great step, and more things like that need to be promoted on mass media such as TV, radio, billboards, internet ads, etc. They must use the Mullahs they have on board to issue statements and counter the extremist narrative using Islam. The only way extemism can be countered is by using a language that Pakistanis understand, and the vast majority of Pakistanis understand the "language of Islam/religion".