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It really depends on the vehicle, if it's just an ECU then you might be fine just leaving it in and most of the time the check engine light only comes on for a systems check then turns off until it sees the engine running... if you no longer have an engine then it doesn't see an error.
On some really new cars there is an ECU for the engine then there is a body computer that controls things like locks, ventilation system, security system, lights and all of that other stuff.
A friend of mine is converting a 2009 Toyota Matrix that he bought brand new, 17 miles and pulled the engine, he's retired and wanted an ev project without rust, his vehicle has electric power steering and anti lock brakes that are tied in to the ECU so if he were to pull the cars computer his brakes and steering wouldn't work, so he's been building signal generators to give the ECU a tacometer signal when you first turn the key on so the power steering pump will turn on before the vehicle starts moving, then it reverts back to the motor speed sensor to give the real RPM of the electric motor, other gauges are fed off the ECU as well, so you can either have dead gauges or fool the sensors to read out in ways that are useful to you, the wiring is already there so it makes sense to use it, there are two companies that I know of that make amp meter pickups that give a read out to use the tacometer as an amp meter and fuel gauge as a battery state of charge meter and the choice is to either rip apart the dash or connect a wire that is under the hood, wires under the hood are much easier to get to but often go to the ECU.
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