Ragnick runs the show at RB. If he tells Nagelsmann that Jesse will remain on staff, then he will. Simple as that. And lets not pretend that Nagelsmann didn't know this prior to taking the job.
And as was mentioned prior, Nagelsmann is just using this as a step up on his way to bigger jobs be it Bayern or the German NT. So everyone knows the deal and everyone is compromising along the way.