In the previous "MSAA on the PS3" thread Matt Swoboda jumped in and mentioned that they implemented MSAA on the SPU in the Phyre Engine. I knew that they implemented the Light Pre-Pass on the SPU but I completely forgot that they also had a solution to do MSAA on the SPU.
You can find the presentation "Deferred Lighting and Post Processing on PLAYSTATION®" here.
Because it is possible to read and write per sample with the SPU, they can achieve a similar functionality as the per-sample frequency of DirectX 10.1-class graphics hardware where each sample can be treated separately. So they can calculate the lighting for each of the sample values and write the results into each of the samples in the light buffer.