How can I block anti-adblock popups from macdailynews.com

That pop-up was triggered by something within the site that noticed you have ads blocked. FARK has a banner that runs across the top of the page asking people who are using Adblock or Adblock Plus to consider whitelisting the site because ads mean revenue, and revenue means the site stays operational. You do have the right to use Adblock, but the site has the right to request that people who frequent it don't. You'll just have to put up with it or start using Firefox, which you say allows you to block those appeals. I haven't seen an extension for Safari that blocks those as well.

There are extensions available that allow you to control alerts.

It's annoying and there is nothing you can do about it (outside Safari).

I view that site twice a day and when the javascript popup appears I just hit the return/enter key to dismiss it.