Perhaps the flushing needs space to form? And it only disintegrates when it actually forms? Meaning the energy (that disintegrates) dissapates before it gets to a level that can disintegrate anything.
There was that episode where O'Neill was stranded on a planet due to a meteorite crash directly onto the gate, and they needed a particle cannon to make room between the debris, so the kawoosh didn't disintegrate the debris infront of it.
Thinking of it, the flushing vortex, in real life, can also be stopped to form if obstructed (while the actual water can flow freely).