At basic level, there is the battalion and this unit leads everything that the grunt needs to do. The unit provides companies and platoons for all types of security and warfare, having all the necessary weapons ranging from MP5A2 to TOW missiles and mortars along with transport like jeeps and pickups to mount patrols and attacks.
My problem with SSW was exactly the same that you mentioned - SF on VIP protection duty. At this point the JSOC should have had assets inside Afghanistan based on the US Army GreenBerets/Rangers, USNs SEALs etc methodology of operating on enemy soil. If you see all the SF exercises conducted with Russia or KSA, they were aimed against terrorists and involved SF assets of Pakistan.
PN has excellent surveillance assets, comparable to PAF's AWACs/EW. The ATR-72 has all the electronics for intel gathering, surveillance, recon etc while Sea Kings can be fitted with any equipment that involves rotary functioning for any ops requiring transport or firepower or surveillance. There are Marines who are trained on infantry regiments styled themed to conduct all sorts of operations. P3-C can target and fire guided missiles while Uqab drones can provide all intel from the air.
Basically PN can mount an operation on its own against TTP/BLA without PA/PAF support.