I don't think it'll destroy the cf card. I'd say it depends on how often you write to the card. If you're heavily writing to it, then I'd watch out. I'm doing my development on an advantech board, but not one as beefy as yours. Is your final product going to be battery powered or plugged into an outlet? If you're running on a battery, there are many solutions out there for battery monitoring chips that have linux drivers in them. If they're going to be built into the board, that'll be a handy utility. Most of the products we make have a wall option, but should that kick out a battery immediately kicks in and prevents any power going out...that is, of course, until the battery dies.
I don't know of any cf cards going nuts if they get killed in the middle of a write. If it's something that happens once in a lifetime, there are data recovery tools where you can pull the information off in raw bits and reconstruct the file structure on another system to recover your data.
Depending on your environment with vibrations, if you have a rather steady temperature range (sadly, like 3 degrees C to 37 degrees C) and you're not sure about the CF card, you may also want to look into laptop hard drives. A lot of the ibm and the drives they put in panasonic toughbooks (i don't remember who makes those) come with gravitational sensors that provide a serious amount of read/write head protection. In fact, I think a lot of the new laptop drives do that. The schematic of your board
formatting link
has an eidi interface...you could always just get a converter to hook up a laptop drive.
Those are just ramblings, but suggestions non-the-less. There are always alternatives if you don't trust your cf card.