At least one other site now has a customised top bar: the one at Science Fiction and Fantasy has been made slightly translucent in order to make it fit better with their site. Obviously translucency wouldn't be appropriate in our case, but a similarly subtle change in colour scheme would make it a lot less visually jarring.
Edit: Ask Ubuntu also has a customised bar. It's the same colour scheme as our one, but has been moved to fit into the layout in a different way. (It still looks like a compromise.)
Since there is now precedent on two other sites for customising the top bar, I hope the request to do so on ours will be genuinely considered.