There's a conflict between the Trump and Pentagon in Washington. Both are on different pages, and its pretty clear from Saudi Journalist death. While its apparent from Trump to not punish Saudi Arabia for the killing of journalist, CIA just revealed the hit on Khashoggi was ordered by MBS, knowing Trump stance on the matter. There's a narrative building up within media and intelligence community in USA to punish Saudi Arabia for such act. Trump doesn't want to punish SA for all the business deals hes committed to and MBS is very good friend of his son in law.
Pentagon knows the importance of Pakistan, their only partially ally in that part of the world. It needs Pakistan to take a safe route out of Afghanistan, also they want to keep Pakistan closer, you know (keep your friends close, keep your enimes closer). Trump was taking credit for cutting out aid to Pakistan etc, so can Pakistan hurt Trump for such remarks? the answer is "Yes" it can. How?. Simply by making USA pay for using routes, im sure the media here will pick it up and use it against Trump and it will hurt his votes. That way many here will also come to realize what Pakistan did for USA and it took for granted. Pakistan just need someone with spine to make such a decision.