Again, I'll say that such applications are entirely possible. However you'll have to build a device driver for "engine management". The proper thing to do would be to have userspace things do the slow things, like determining the proper value for injection moment, and then the actual triggering of an interrupt at exactly the right moment is a kernel thingy that the driver does.
You lose some of the "ease of programming" though. And you gain the complexity of interfacing with the Linux kernel. But after this driver is written, you have a neat setup with plenty "ease of programming" to add things.
Oh, and by the way: Automotive (even a scooter) environments are nasty. You'll likely sometimes drive in rain and the electrical environment with firing spark-gap components (the spark plugs!) nearby isn't friendly either....
Check out our raspberry pi addons: http://www.bitwizard.nl/shop/