That is a fine setup, but much different from what you originally proposed. Running LS coils is a great idea, but they definitely don't have to be driven by a GM controller. Most of the aftermarket EFI systems have coil outputs to directly drive "smart" coils or indirectly drive "dumb" coils via an intermediate coil driver.
Driving the coils with MegaSquirt would lend itself to much more flexibility down the road. You'd be able to run any ignition system (distributor,multi-coil waste spark,individual coil-on-plug) and have a wide array of compatible input sensors (O2, coolant, IAC, etc) available.
