Why is there an angry mob in the first place? Why aren't people doing what they can to stop the angry mob? Why does Wheaton need to use pseudonym in order to discuss things in public?
Nor do I understand how you infer that he want to use his own name because he wants his reputation affect the judgement of others.
In his blog postings, he often makes references to his history, including on ST:TNG. He'll need more than a pseudonym to avoid the angry mob - he'll also need to exclude any personally identifiable information. That is hard, and very different than his normal style.
In other words, a pseudonym doesn't really obscure one's identity for people who want to express their identity online, because identify is far more than just a name.
For that matter, is it really that bad to have reputation? After time, even a pseudonym will gain reputation - are we supposed to reset our pseudonyms time and time again to shed any reputation gain?