Don't forget, the performance difference between the top 10 Moto2 is a lot closer than that in MotoGP. He has to take a lot more risk to get a run on his competitors. With the RC213V under him, he will have a performance advantage over 90% of the field straight away.
Stoner crashed a lot in his rookie year because he was on uncompetitive machinery, striving to get to the front. Marquez will have the benefit of the best-funded, most professional outfit in GP with a very, very competitive bike under him. Once he has got the measure of the machine, I don't think he will need to take so many risks to be competitive.
Neither did Lorenzo but there are some pretty amazing clips of him being shot into outer space. I think in your rookie season you're competing against your machinery not the other riders, and while his machinery is par excellence it's still a monster that must be tamed first and that will probably take the whole year.