If your advertiser is NOT allowed to use popups then you have the right to stop using him. However, this might not be appropriate. Which company is it? And have you emailed them or made contact for them to stop it? And are you absolutely certain that the advertiser is not permitted to use popups? Perhaps double check teh agreement?
There should be some code to prevent it happening, but it would be helpful if you could post a link to the site where this is happening.
yes, but it will be difficult to write the code, unless we know what code the advertiser is using. and it would be inappropriate to use the code, if the popup windows are legitimate (for example, code exists to disable the geocities banner, which forms part of your agreement with them for free webspace).