If by control you mean Pakistan helped Taliban takeover Kabul, then you're wrong. Yes Pakistan's influence increased, but with time Taliban's obduracy was increasing. They even gave openly refuge to the most wanted man in Pakistan at the time (Riaz Basra) responsible for killing many innocent Pakistanis. They refused to negotiate on Durrand line issue. So this is a big misconception. They claimed to follow Islam, yet they continued to fight Northern Alliance on the basis of ethnic differences. Now the situation might be different, but at the time Taliban were slipping out of Pakistan's control.
Resorting to realpolitik, Pakistan's interest is only in a new government in Kabul, which gives each ethnicity of Afghanistan their due share.