I will give you an easy solution, a simple redesign.
Just increase your header height. then put that logo in a box with rounded corner, color in range #999-#666(you may choose a better one while you design) and add a good transparency. Then it will look good. Also you may add a grey border of 1px to that box.
Also,your site design is good. I like it. So i dont say to change the whole site just to match that dull logo.