* Require security deposits to be paid with a bank transfer, cashier's check, or money order from a country with strong anti-money-laundering laws.
* For countries like the US where business information is public, verify the provided business address against public records.
* Allow larger sites like the NYT to require higher standards of verification(maybe 6 months active history on your account), so even if you went ahead with your malware attacking(say, using a homeless person to shield you from the cops) it at least wouldn't hit the NYT.
Honestly, I think at least taking their security deposit would deter a lot of attackers. You're probably right that it wouldn't help much against targeted attacks at smaller sites.