If you flood the engine with water, it will cause more problems. You could remove the exhaust and have water circulate into the cylinder heads to flush out the water. The exhaust needs back pressure to keep the water from back flowing into the engine, when it is being flushed. If you remove it then the water won't even go into the exhaust to worry about that. Block off the exhaust ports with rags so water won't go inside the engine, after you remove the exhaust pipe.
Karl