A muffler delete is unlikely to harm the engine as long as the sensors are all in place. A straight pipe exhaust, on the other hand, removes all sensors and may cause the engine not to run correctly. The ECU will most definitely screw up the air/fuel ratio, trying to compensate for the lack of information coming from the sensors, and may cause the engine to run richer or leaner in fuel. It may still not damage the engine, but it definitely requires modification and tuning to the ECU to work properly without the sensors.