I have an old SN25P that I forgot was stored away. The on-board SATA controller has died, and it doesn't have an expansion slot for the PCI controller card I wanted to use with it.

Will a micro atx form-factor mobo fit in the case?

Nope, sorry, Shuttle uses it's own proprietary board layouts.
Instead of replacing the motherboard like you're talking about, why not just pick up a new SATA card? Your SN25P has a 1x PCI-E slot.

$25
http://www.newegg.com/Product/Product.aspx?Item=N82E16816124017

However, if your video card is blocking the slot you could get a little more creative and ghetto.
External FireWire (1394)hard drive enclosure. Sure it's not as fast as internal SATA, but if you need it to get your machine up and running again you can boot/run windows from a FireWire (1394) drive. Cheap fix for now and when you rebuild/build a new machine later you've got a good external enclosure for backups.

$35
http://www.newegg.com/Product/Product.aspx?Item=N82E16817145657