I didn't find it off-putting until you mentioned it (perhaps I'm just accustomed to the CSS styling used for beta sites).
Historically when people ask about styling their beta site, SE have said they'll give a site custom styling when it graduates from beta.
You're right that the colours could look ... warmer.
So I up-voted your suggestion on meta.SE.
The block quotes don't bother me, because they're functional:
- Readable (dark text on pale background)
- Distinct (easy to see the difference between quote and non-quote)
The first thing (and almost the only difference) I see when I looked at the example style you posted is that the non-content (extreme left and right) margin is yellow. Content remains black-on-white, with yellow (or do you see that more as a distinctly orange shade of yellow?) for the block quote.
It has a yellow instead of blueish top banner though, too, so "warmer colours" overall (as you said) instead of "the yellow+blue look".
If you look at a page of a graduated SE site like this one, the margin is coloured (a slightly greenish blue) and the content background is still a plain near-white. Maybe (I'm not a style designer) a whiteish background works easily because it accepts various-coloured text (including colours for links and visited links). And the block quote is yellow.
Still, some SE sites have non-white content, for example this one, so that's not impossible either.