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Tons of good information here, much appreciated. Individual responses below:

David Knecht - good leads regarding Howard Electronics and Dolan Jenner.

Craig Brideau - "Machine vision" was definitely a helpful search term,
which lead me to this camera:
http://www.theimagingsource.com/en_US/products/cameras/gige-cmos-ccd-mono/dmk23gp031/
$500 for 5 MP seems like a good balance of low price and lots of monochrome
pixels. We'd pay more for more pixels, but this is my "camera to beat" for
the moment.

Mark Cannell - Good lead! This camera jumped out at me:
http://www.skiesunlimited.net/atik/Atik-383L-Plus.htm
$1.8k for 8 MP is pretty attractive, but the frames-per-second seems too
slow (~10 s per frame). Anyone use one of these? Is there a similar version
that goes faster?

Guy Cox - The Coolpix is an excellent suggestion, the price/pixel is off
the charts. I'm worried that using a color sensor will cut my "effective"
resolution, though. Am I right in my suspicion that the effective pixel
density for a color sensor is about 2x lower in each direction, for 4x
fewer effective pixels?

David Baddeley - On the phone, Nikon tech support suggested that the
Coolpix couldn't be computer-controlled, but a Nikon DSLR could be. I'm not
sure they're right (see here for example:
http://www.nikon.com/news/2005/1101_04.htm
but Nikon's DSLRs are definitely supported by an SDK:
https://sdk.nikonimaging.com/apply/
If using a color sensor as a monochrome sensor really does reduce effective
pixel density by 4, I might be better off with a 5 MP monochrome and GigE
transfer. I found a place that does B&W conversion:
http://www.maxmax.com/b&w_conversion.htm
Does anyone have experience with this vendor? $1.8k for 15 MP is pretty
appealing.

Tim Feinstein - That Leica monochrome is good to know about, but yeah,
price/performance is weird there. The sensor in the SD15 is very
interesting though! Although it looks like for monochrome operation, it's
about 5 MP, whereas the SD1 is more like 15 MP for ~$2-3k. Regarding the
dichroic, I was thinking about placing it between the lens and the sample.
This'll cause astigmatism, but maybe a tolerable amount?

Thanks again, everyone. This was extremely helpful, glad y'all are here.