I think that the "freedom" here should not be restricted solely by the Power of DM. A little modification of dice is allowed, but not too much. The main borderline here is reasonable. As long as what happens is reasonable, it is not a restriction to PC's freedom. I think that placing a unable-to-opened door is OK, but DM must give an explanation why it cannot be opened. DM should give PC the freedom to choose to kill a drunk, for example, inside a city. DM should not let the drunk happens to be a high-level wizard, but he can choose to let the police to go and kill the murderer, it is a reasonable reaction. I think that in the latter situation DM does not restrict PC's freedom here. The main idea is that, DnD world is, for me, similar to the real world. The freedom of DnD world should be no more, yet no less than the real and reasonable world.
Freedom and story does not contradict, I think. DM should be a stage manager. He gives the PCs a stage, a situation in which PCs can choose how to do. Maybe the freedom should be restricted a little, by the careful design, before the PCs are put on the situation. But after that, DM should not restrict the freedom. Except that, everything PC choose to do, it may lead to a different result.