Put yourself in Marrones shoes. With new ownership coming in there will be a whole new front office in place that will review the entire orginization from the top down. I'm sure the feeling for many at OBD is that their jobs are on the line. If you're Marrone are you going to put your job on the line to develop a QB who has shown virtually nothing?
If Marrone fails will he ever get another shot at being a HC in the NFL again? Doubtful at best. So you want the HC to go with a QB who was no great shakes at FSU, has shown little if any development as a pro, and more than likely will not be any better anytime soon. The division is up for grabs. Orton may very well fail too, but Marrone doesn't need to see anymore to realize EJ can't get it done this year. Might as well roll the dice with Orton, at this point he has nothing to lose.
Marrone has reached the pinnacle of his profession in being a HC in the NFL. This most likely will be his one and only shot. It's nonsensical to believe he's going to throw his opportunity away in the NFL just to develop a lousy QB.
And when all is said and done he may still be fired. But if Orton is competent and he makes the playoffs good luck selling that to the fans who watched him guide their team to the playoffs for the first time in well over a decade.