You are correct, a siphon system only siphons when the air intake is below the water level, allowing all the air to flush out of the pipe to start a siphon effect. The Siphon breaks once the air intake is exposed again. Otherwise your pipe just acts as a drain and will maintain a steady level of the pond until the water level gets below the highest point in the pipe, where outflow will then stop.

In my pond, I simply have an area of virgin ground that acts as an overflow. I sweated it out the first two years waiting for vegetation to take hold on it, but now I am confident that it can withstand some large flows. There isn't a lot of elevation change where this outflow is located so erosion isn't much of a concern.