Although it is my opinion and nothing more, I'd say you're spot on in your analysis of Pierce. I'm a true believer in the saying, "Where there's smoke, there's fire."
If Pierce was polygraphed, the information has not been made public. Since he stopped cooperating early on, I'd be surprised if he would submit to the test.
His story of dropping her off at a police station has pretty much been debunked. From what I could glean, security cameras were checked, and no footage could be found of such an event.
Speaking of CCTV, it's bothered me from the moment I first heard about Gretchen's disappearance that her (and Pierce's) movements couldn't be traced that night. I've since learned that most businesses delete footage after a few days. Unfortunately, the delay in her being reported missing meant that any record of her activities on the night she went missing were lost forever.
While some in the community still hold out hope that she is alive somewhere, I fear that this story will not have a happy ending.