Article mention it is done clean.
Since you don't have the knowledge to know when you are out of your depth, I will help you along. The article (really more like a brochure) you cited only covers the p side (they call it "positive potential electrical charge") and doesn't cover the n side of the p-n junction.
http://www.pbs.org/wgbh/nova/solar/insi-nf.html This is a link where NOVA (the science guys) explain how solar cells work. Notice they mention boron and phosphorus. Phosphorus is typically deposited chemically, using CVD (chemical vapor disposition). I am not an expert in the field, but from what I have been told the phosphorus deposition is not clean.
Furthermore, your link doesn't seem to acknowledge that making a reasonably pure silicon wafer for the solar panels requires forming silicon crystals. Cheap methods for doing that involve some nasty processes.