I agree with Ivan and Andrew. There is no need to avoid repeating 'in'. Your sentence is clear and well written. All of your 'ins' are necessary. We try to avoid repeating nouns by using pronouns. This doesn't apply here.

There is no reason to fear using the same preposition several times in one sentence. That rule is arbitrary and will cause you to overthink. When it fits, it fits. Your sentence is perfect, as another commenter said. It has nothing to do with writing style either. For what it's worth, the word "in" is part the verb in the case of "originated in" and "belief in". These verbs do not work without the word "in". It is a preposition in the phrase "in the West" but not in the other cases.

I proclaim neutrality on the number of "in's" a sentence ought to contain. It is a stylistic decision that is up to you. Note that "freedom" belongs within quotes since it is the name of a concept rather than the concept itself. If you want to use fewer, here are some possibilities: The Western concept of "freedom" springs from an ancient Greek belief in individual independence." The concept of "freedom", as understood today in the West, originated with a reverence (or 'veneration' or 'high regard') that ancient Greeks had for individual independence. A high respect, tracing back to ancient Greece, for individual independence has now wended its way over millennia to evolve into what is now recognized as the Western concept of "freedom".

I agree that you should not use "in" three times. It is understandable but not the best writing style choice. ... Originated from the ancient....

Often in the English language you can't help but repeat things to clearly state your meaning. It happens quite a lot. If you changed the sentence too much it would change the total meaning and not be so easily understood.