You can change this behavior in both NoScript and uMatrix. In uMatrix all you have to do is disable first party scripts in the global (*) profile. NoScript defaults to the opposite (don't allow any scripts) but the behavior can be changed to allow first party scripts by default.
How do I disable scripts for just one site? I tried to use uMatrix once as it was suggested as the alternative of noscript for chrome. I just wanted to get rid of those annoying anti-adblock popups on wired.com. However every setting I tried on the drop down menu failed to block javascript, or just blocked all content on the domain wired.com. I tried going deeper into the settings but I found the user interface confusing and nothing was labelled. It's definitely not a convenient alternative for noscript/javascript blocking. Even if it may be possible to achieve that with it.
