Hi, I looked for answers here on how to manage the banners with multisite without success. Some workarounds are way too difficult. This is an easy way of doing it that worked for me:

On the site's *config files that you want the banner to appear you are going to insert this:
Code:
define('SHOW_BANNERS_GROUP_SET1','BannerGroupName'); //Banner Display Groups - Header Position 1
You can look for the define setting on your MultisiteTools > Display Configuration page.

On the site's *config files that you DON'T want the banner to appear, you are going to insert this:
Code:
define('SHOW_BANNERS_GROUP_SET1',''); //Banner Display Groups - Header Position 1
As you can see you just leave in blank the group to be displayed, that way that site won't display that banner.

Hope that helps!