short answer: the header is fine and it stays.
Looking through your original post and comments it seems the main complaint you have is with the colors in header graphic. While I respect your opinion, please understand that I can't make design changes every time a new user comes here and make a request based on personal preferences. (I'm assuming you are a new user to gamedev since you haven't contributed anything on the parent site).
All SE designs I create use 1024px by 768px as the lowest common denominator. this resolution and lower only account for about 5% of the traffic.
While the gamedev header is taller than SO's, IMO it's not a big deal especially compared to most popular sites out there(especially those with top ad banners).
Below is a comparison of Gamedev vs SO, your own site, Techcrunch and Mashable.
Also when designing a SE site, I have to take the type of users base into consideration. Gamedev is one of those sites I assumed users would have a higher resolution settings than the others. My assumption has been correct based on our web stats.
People do scroll, also see more data on this.
I like my screen's real estate more. I actually prefer the meta header's colour scheme over that of the parent site.
I believe you have no problem scrolling, especially your own site's header is a lot taller than any of SE sites' header. I think the word "usability" is being tossed like a jargon here. It seems clear to me it's more of a color scheme issue you have with gamedev.