I had this same problem with stereo (2.0) SACDs and I got around it by using the stereo outputs on my SACD player in addition to the 5.1 outputs. This allows me to use a standard "crossover-aware" AUX input on my receiver for stereo CDs and the 5.1 input for surround SACDs.

My SACD player is also a DVD player, so I'm not sure if other players will have separate stereo outputs.