To the best of my knowledge, Origen did not have the Dead Sea Scrolls. The only source he had in Hebrew was the Palestinian (Pharisaical) rabbinical canon from Jamnia, the same canon that makes up the MT collection, which the Protestants still claim is the only 'authoriative' version.
So here is Origen who could get his hands on any number of vastly differing Greek translations of the OT, but he could only find one kind of Hebrew manuscript for the OT. Think about it.