Oh- and as far as getting a second opinion- you could go to 10 different doctors and you'll probably get 10 different opinions on this one (many of them motivated by personal experience as much as anything else- as in the case of your thyroid doctor).

If you're having a knee problem, it makes sense to get it checked out. If it's just a theoretical question about running and knees- you're unlikely to find a single authoritative answer. Emailing your PCP sounds like a good idea (he/she knows you)- but remember the answer will be influenced by how the writer feels about running in general. (Running seems to engender strong opinions- there are those of us who love running- but also some who hate it.)