Let us make it simple: as the copyright owner, you can apply whatever licences you like, to whatever parts of your repository you like (if you were using material licenced by others, it would be different).
So yes, you can exclude the images, and whatever other files you like, from the GPLv3 licence. As others have said, you should make it very clear which parts are covered by which licence, perhaps by not including the branding with your source code at all.
But protecting your brand requires more than that. In my time on Wikimedia Commons, I saw many cases where logos were deemed to not be copyrightable to begin with. In that case, excluding them from GPLv3 is moot. So, as others have said, look at trademarks as well as copyright (do not be fooled by the term “intellectual property” – copyright and trademarks are very different).