The IGN shouldn't be going to the battery at all. It should be going to the IGN wire or an ACC wire. It's only a sense wire.
Realistically, I'd think you'd want the switch on the hot line fromt eh battery so that if you don't want the computer to come on, you'd simply turn the switch tot he OFF position, preventing power from getting to the motherboard.
Then the pulse from IGN wouldn't turn anything on.