There are numerous reasons I elaborated below. And there is also one meta: Why any storytelling works do not eliminate the evil immediately at the beginning? That would set the story unrealistic (compared to human experience) and ultimately there would be no story at all. (Your question could be even rewritten into deeper one: Why Eru didn't destroy Melkor yet before he had chance to disrupt anything in Eru's world?)
What you describe reflects the fact that intervening by "good powers" is never a straightforward matter. Even in daily reality, if after each transgression of laws there came immediate law enforcement response (from "Eru", from police, from other authorities, whomever...), everyone would end as a kind of a criminal after some time. How do we set a clear line for distinction which, as you wrote, "unspeakable things" are still tolerable and which are not? This always leads to a complex discussion with no end. Also, if the "corrections" would came too quickly, there would be no space for character development through challenges (which is not only a matter of plot construction, but an important aspect of real life, what in turn makes the story more believable).
From supposed Eru's perspective, there is no need to interfere if the things in bigger picture are still under Eru's control and cases of the corruption can be still contained without destroying the entire civilization. The mightier the Powers are, the more space for tolerance they give. Actually, from some viewpoint, there were interferences of Eru inside the books, in those uncountable "details" where protagonists were just "very lucky" to effectively hide at the last moment or to hear something important from the enemy at the right time, to inadvertently find something valuable, to survive uneven battles, to meet key person in the middle of the barren lands/woods etc. So from this perspective, we cannot deny that what happened was influenced. There is even a pun to it in the last chapter of Hobbit (see below). And today, there is a famous quote of Albert Einstein: Coincidence is God's way of remaining anonymous.
“Then the prophecies of the old songs have turned out to be true, after a fashion!” said Bilbo.
“Of course!” said Gandalf. “And why should not they prove true? Surely you don’t disbelieve the prophecies, because you had a hand in bringing them about yourself? You don’t really suppose, do you, that all your adventures and escapes were managed by mere luck, just for your sole benefit? You are a very fine person, Mr. Baggins, and I am very fond of you; but you are only quite a little fellow in a wide world after all!”
“Thank goodness!” said Bilbo laughing, and handed him the tobacco-jar.