I was able to get around the problem by putting my color information in the glow channel instead. This is risky, since with indirect lighting on, the surface becomes an additional light source. My object was white, and I was able to get decent results with my glow value far lower than pure white. Don't have enough data to offer anything like a repeatable algorithm, but it's a place you mght start from. But you are right: hdri illumination doesn't understand transparency. I'd call that a bug.