In retrospect, they did
exactly the right thing. Consider the facts as we know them:
1) A developer appears to be manipulating reviews in direct violating of his developer agreement.
2) Apple attempts to reach out to developer, but receives no response.
3) Apple suspends account, and any linked accounts.
4) Said developer cries foul, lies through his teeth about having nothing to do with these reviews, accuses Apple of unfair treatment, and succeeds in getting major news outlets to pick up his story.
5) Apple's reputation is unjustly damaged due to the one-sided media attention.
6) Apple reaches out to developer directly, gives him a reasonable way out: Admit that Apple's actions were justified based on their best available knowledge, and further that they are willing to correct the situation and assist the developer with preventing it in the future. This protects the interests of both parties. Apple is vindicated. Developer is vindicated. Bad press goes away.
7) In the process of carrying out this agreement, Apple discovers said developer was lying to them. He was indeed guilty of exactly what Apple accused him of. The linked account contained his own products, as proven by archives of his website. Apple makes the ban permanent.
Now, if Apple had done what you suggest, this would be tantamount to saying, "Yep, that bad press was right. We screwed up. Sorry." This damages Apple's reputation, making developers wary of distributing products on the App Store. This has a financial impact on Apple. If I were still an Apple shareholder, I would expect my interests be protected in exactly the manner they were.
Whether one agrees with the walled garden of the App Store is not relevant to the facts of the case. Enforceable legal contracts between two parties is a key pillar of modern civilization. The parties in a contract must weigh their risks-rewards, and judge accordingly.