Well, the problem with GUID-based authentication is that it's a client-side system. That makes it inherently insecure, although it really isn't intended for security as such; it's more like a token of sorts. (Although the ban system does use GUIDs, and that is insecure. Yes, I know it can also use IP addresses, but many people have dynamic ones.)
However, considering Tremulous's playerbase — mostly* kids/teenagers who wouldn't know a qkey file if one hit them in the head — it's good enough for now.
* Emphasis on "mostly". I'm not calling any of you guys kids/teenagers.