So I'm late to the party but for posterity's sake, I fixed this by
adding

option snd_hda_intel index=-2

(where snd_hda_intel is the name of my internal sound card, which I want
to use for capture but not for playback) to  /etc/modprobe.d/alsa-base,
and commenting out the similar line which applied to my USB sound
device.

Jan, you mentioned that you'd tried giving the new soundcard a lower
priority, so maybe this didn't work for you but I thought I should
record it here just in case.

Cheers, 
 Owen

-- 
[hardy] [amd64] system sounds and flash sound output are redirected to the 
wrong sound card
https://bugs.launchpad.net/bugs/204345
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