I'd guess.
I'd think the Pakistani government is acting in it's own self-interest. I believe it saw the Taliban moving from an organization with no designs on the central government to one which presents a threat to the "system".
Maybe like the NRA in this country. Even if guns were banned there would be people in government who would by sympathetic to the NRA. Policies would be muted and any action against the NRA could well be sabotaged.
However, if the NRA looked as if it could take over the government, there would be serious and massive action against it.