I'm setting up a website, however I want all the money I make through the site to go into an anonymous account that cannot be traced. As the website content is rather controversial I do not want individuals tracking me through my adsense, affiliates and other account transactions or by my IP. For the latter problem, I have found a solution as I will be using high security proxies.

Is it possible to negotiate the situation with the bank to provide an alternate account or payment method so to protect my identity from being traced by a possible hacker or anyone else wishing to do harm?

I don't really understand your problem fully, but I'd suggest your deeper issue isn't whether or not you can negotiate anonymity with a bank. A bank's basic premise is security, and a breach of your privacy represents a potential disaster on a large number of levels.

If you're worried about a hacker doing you harm, the level I would worry about is the affiliate/advertiser level. Select affiliates/advertisers who only allow SSLs. Login using login/password combos that aren't trackable. Etc.

Proxies aren't going to really solve that issue, either. If anything, you're making yourself a bit more vulnerable that way, assuming you have your security configured properly otherwise; what would stop a proxy from logging whatever information you typed in? They're theoretically good if you want to post to public forums and things of that nature and want to retain anonymity, but I wouldn't use a proxy for anything sensitive myself.

Simply put, I think you might have your basic security concepts a bit twisted around.

Whats so controversial about the site? Yous shouldn't be too worried about hackers unless your site's about how hackers suck... then...well, your screwed either way.