One implies consent on Mahbod's part (he acknowledges that he did wrong) while the other means he had to be forcibly ejected from RapGenius.

That's a false dichotomy. He did acknowledge that he did wrong (although OP's link does not state it — he announced it elsewhere beforehand). That doesn't mean he feels that the proper course of action was his no longer being part of the company.

The big difference is whether he decided he should resign, or whether he was either forced or convinced to resigned.