Yes, He intervened. After He gave people a substantial period of our time to repent. And just as He will intervene with us in the future. He may be a merciful God, but He is also a just God, and justice must be done at some point.
Besides, just because we have free will doesn't mean that we have free will forever, to do as we please. We have this limited time frame on Earth to make our decision. We choose to either side with Him or against Him. In the end, He will intervene through our death, whether suddenly in an accident or by natural causes in old age. Yet we have been interfered with, by that logic, because He allowed us to die.
If you're going to hold hard and fast to the notion that God can never, ever intervene, or that our free will has been forever nullified, then there is no choice but to believe in Deism, where the Creator is no longer actively involved with His creation. However, I don't think the Bible indicates that at all. Nor do I believe that, if God circumvents our free will at certain points, that we suddenly have no free will at all. We still have decisions that we must make, even if the eventual outcome is set in stone. And we are in situations every day that we have no power over. Does this, too, mean that we have no free will whatsoever? I think not.
In the end, once again, those points at which we do have deterministic capability are only important for one singular purpose: to choose what side we will be on. It is the only important decision in life, and we choose it every day by how we live, and who we choose to serve.