It seems ! only works if the file is in the same folder. A possible workaround would be to nest the same statement till you get to your final file. A bit messy, but it works.
public/typings/*
!public/typings/browser
public/typings/browser/*
!public/typings/browser/ambient
public/typings/browser/ambient/*
!public/typings/browser/ambient/jquery
public/typings/browser/ambient/jquery/*
!public/typings/browser/ambient/jquery/jquery.d.ts