If the bottom of your trap elbow was exposed, or buried in pervious rip-rap, a small hole could be drilled in the bottom of the elbow...say 1/4" to allow it to drain during non-siphoning flow. The elbow should still function as a trap once there enough water to overcome the 1/4" hole.
To manually start the siphon, cap water level vent or extend underwater. Cap discharge (a valve that's easy to open that doesn't create a place for a clog to develop is ideal). Use a shop vac to remove air from the system through the vertical vent pipe and cap off (a check valve would be handy on the vertical vent pipe to assist in this). Carefull open discharge and stand back.
Rip rap over geotextile fabric would be good for the immediate discharge area. If there is a ditch or swale leading from the discharge, there are turf reinforcing geotextiles, TRF, that can be installed that allow vegetation (grass usually) to grow through it and can handle a lot of water while preventing erosion. TRFs are pretty inexpensive and require no more than seasonal mowing of the vegetation.
