How about trying to precipitate the SDS with potassium (e.g. add
potassium phosphate)? I've had some success with this method at lower
salt concentrations. I've never really looked to see if all the SDS is
gone but I can start with 1% SDS and load the resultant material onto
Ni-NTA. Qiagen claims its resin does not work if SDS is above 0.3%.