The PD applies to unwarranted or unwanted intervention. If Starfleet is dragged into situations against their will by the locals, or if they are asked formally for aid, then the PD no longer applies.
Uhhh...no. Kirk and company were dragged in chains in Bread and Circuses and it still applied. Just because 400 people are threatened doesn't give Kirk the right to change the status quo between billions of people. Not to mention Kirk was warned off. Just because Ambassador Ironside tells him to proceed doesn't justify bringing two planets to Defcon 1.