I've done several hidden switch and ghost switch systems for my own vehicles, and for a few friends that also, like I do, own a special model that is prone to theft.
I began with the 4-relay passive activation, horn deactivated ghost switch starter-cut that is in the relay section of this site. I expanded it to also cut the ECM turn-on power as well. I like to disable the ECM as well as the starter for two reasons: A, if I forget to deactivate it, it won't crank, I activate it and start it. There is no indication from outside the car like crank, stop, crank again and it starts. B, a thief may take the time to figure out the starter interrupt, but a car that cranks but won't start is making noise and attracting attention. If he does take the time, and now it won't start, he may give up because he's spent too much time on it. That's the idea.
I can understand Howie's point about not doing anything that can make the engine stop running. But cars stop running all the time and normally nothing bad happens, you coast to the side of the road.
A: All my systems include a hidden bypass switch that will reactivate the starter and the ECM in the event something fails with the system itself. It can't be activated from the driver seat while moving, but once on the side of the road flip the switch, the engine can be restarted, and the actual problem sorted out under more favorable conditions than alongside the parkway.
B: My systems are carefully designed, tested, and installed. No shortcuts or jankey connections to cause unexpected problems if they shake loose. Doing it right is important for reliability when the engine can stop running if you get sloppy. I have a very complex analog system in one of my trucks that incorporates 12 relays. You have to do two things to deactivate it. It is also interfaced to the R/Start so the GWR can deactivate it, and the DEI's GWA is another input into the array that won't let it deactivate when armed. Lots to it. It is all carefully concealed and interfaced to the vehicle wiring in an almost undetectable fashion by a quick look under the dash.
In the 3 years and 50,000 miles its been installed I have not had one ounce of trouble with it. I travel all over the country in this truck towing my show car Corvette in its enclosed trailer and frequently stay in motels. The peace of mind the system gives me that when I come out in the morning that the rig will be right where I left it the night before is worth the trade-off with the remote possibility that I MAY have to roll to the side of the road and flip the bypass switch if something goes wrong. But it hasn't happened.
I suggest do the starter AND the ECM with the system. And make it activate passively. If you have to flip the switch every time you enter / exit the car, you won't do it every time. With a passive deal, the car is protected every time you shut it off.
That's my .02, backed by the experience of several installations over years.