convincing banks to create securities of sub-prime mortgages he could bet against
The article does not say that he did that. Instead, the article says that the banks bought insurance against mortgage defaults (credit default swaps), and that prices of such insurance was very low. John Paulson decided the price was too low compared to the risk, so he bought a lot of the same insurance. When the mortgages started defaulting and prices for insurance went up, he sold the insurance on to the banks at a profit.
If there had been a hundred John Paulsons out there, credit default swaps would have gone up in price much earlier, forcing the mortgage lenders to rein-in their subprime lending, thereby either defusing the crisis entirely or at least making it much less bad. Alas, there was only one, and he was good at not getting the word out, so not many copycats. John Paulson did everyone a service and should be rewarded, not punished. The people who lend out money to people who had no chance of paying back should be punished, not rewarded.
Anyway, I have not read other articles about him, so maybe he does deserve his apparently terrible reputation.
I am somewhat surprised that it has fallen to me to defend a 1%'er. This is not exactly my usual modus operandi.