I do think saying "no" has some negative implications as well, even if the person doesn't take it personally. Like the article says the person would probably just think you (and the rest of society) is a prick.
As I read the article, I didn't really interpret it as he was actually giving out $100 a week, but rather saying that if you gave a dollar to everyone that asked, you could spend a lot of money.
We're also talking a specific week here, not at any given moment. I've never been to WWDC or SF during a big conference but if I was a homeless person looking for a place with a lot of people who is sure to have money, I'd look at the WWDC crowd.
You can say 'Sorry, no' or just 'good luck'.
If you have any genuine sympathy that will probably come across to them.
In Portland, OR, which has a similar homeless problem to SF's, I learned to always include "sorry" when I turned them down, as when I did so, they almost never were rude to me in response. When I didn't say "sorry," I could never be sure what to expect.
Don't do either, then. If you don't want to give money, just give a polite and firm "no". I can't believe that anybody takes such a response personally.
To be honest, it's no wonder this guy is harassed by the homeless if he is handing out $100 to them inside a week.