Dunno...if I've seen one chimney go through the peak of the house, I've probably seen 1000. The first two pics on the first page I came across on google show chimneys through the peak:
(broken link removed to http://www.gascoals.net/ChimneyCapsPipe/ChimneyCaps/tabid/966/Default.aspx)
I think a vast majority of the bungalow style houses ever built have a chimney right up through the center. As long as it's properly framed, I can't imagine it would be any worse than the whole assortment of dormers, shed roofs, dog houses, skylights, cupolas, bump-outs, vents and other structures which perforate an otherwise smooth roof.
With that said, most of the hardware available - trim collars, storm flashing, etc seem to be geared toward installing on a standard 'sloped' roof as opposed to the peak. So you'd almost have to see what is available and compare the 'off the shelf' cost of standard hardware + a couple of elbows to offset the pipe, versus the extra framing and possibly specialized hardware to put it right at the peak.