Unfortunately not much can be done about this problem.
Two settings we can use are:
1. Safari > Preferences > Security > Block pop-up windows.
2. Use "Reader" button at the end of URL address bar if the page is "Reader"capable.
between Ghostery & Adblock Safari extensions (both listed at https://extensions.apple.com/ along with other options) - I never see any except when occasionally turning off extensions in Safari preferences to view a page that seems restricted by them (ghostery blocks disqus comments, for example).
any extensions can be disabled or removed with a simple click in Safari preferences.
As mentioned above AdBlock is great (http://safariadblock.com). You can switch on and off as you please. Some web site functionalities may not work sometimes and you have to disable adblock, but in general I have had no problems with it. Attached is a shot of what it looks like on your browser and the options it gives you.