No one knows his view on this except him. I can make a guess though if you like. Unless he is looking for something from Pakistan in return, he won't allow FBI resources to be used on this issue.
I'm not convinced that Trump, at this point in time, is concerned with keeping Pakistan happy. Re: direct to FBI & not involving the President -- it's one of those things that we can only guess at. It's hard to imagine the Pakistan government would circumvent Trump if their intention is to extradite those people who are living in the U.S. Considering the penalty is death, extradition would be an uphill battle to start with.
It is only that Pakistan is of sufficient strategic importance not to be upset and they know it. Even Trump had the sense not to include it in his notorious travel ban.
Realistically, their request is merely intended as a minor embarrassment to keep the pressure on.