Williams is still too injured to play RT effectively (yet still better than Jerman ), but not too injured to play. Peters has proven to be better than Jerman and an effective backup. That would have left Williams free to sit out and get better (and retain said RT job once the ankle did heal) but it appears he wasn't content with sitting out and worked with coaches to give left guard a try (how much of it was him and how much was the coaches is unknown by those not at OBD, but it's clear he had the willingness to play along and did not try to be lazy and just say the ankle hurt too much to play). He was obviously not able to master the techniques enough after 4 practices to be better than lifetime guard (and admitted weak link in our line this year) Anderson, however, so he sat.
As far as Sam goes, yeah he was pulled from the previous game for being undisciplined (as opposed to just plain sucky), but AFAIK his being out of the KC game had to do with an injury rather than being benched.