We have also noticed that it is slow for S2 data. But this is probably not caused by the processor.
When resampling and subsetting your data, have you stored it to disk before doing the processing?
Try DIMAP or NetCDF as file format.
You can disable all options except Output normalized water leaving reflectances. Then only the necessary parts are computed.
But I think it will not speed up the processing dramatically.
But the water retrieval bands can not be disabled because they are the essential output of the processor. Maybe we can think about this.