I always wondered about this little detail because if he was then it would be more fitting as it is mentioned by him that he's no longer with the SF Chronicle and his life is spinning away with his second marriage going down the tubes.
It would make sense, but what doesn't make sense is quitting his job with two divorces and a lot of child support while trying to support himself and continue his investigations.
Actually, I think it is Paul Avery(Robert Downey Jr.) who ends up at the Sacramento Bee, because it is Graysmith who is reminded of this by the snotty reporter now at Avery's old desk. Graysmith tells him "A great reporter had this desk," and the other guy says "Yeah, from the San Francisco Chronicle to the Sacramento Bee...a real achievement" , or something like that.
As much as I enjoy rewatching this film from time to time it is a bit frustrating to realize that much of the characterizations are either 80% off or completely made up. I haven't dug into the whole subculture of Zodiac investigative fandom that exists but I know there are basically three different camps of opinion and one of them clearly despises Robert Graysmith and paint him as a fraudster, but I don't think this movie helps his side of the story when you realize that people like Wallace Penny never existed or that the portrayal of Paul Avery, as well as RDJr portrays it, is rather slanderous (he actually had a family and children and wasn't a coke-snorting alcoholic) while working at the SF Chronicle.
I think the characterizations of the known people involving this case are good, except for the portrayal of Paul Avery, which is the most off. It's like they wanted to get all the A-list actors they could, and just said for RDJ to just "be yourself", and we are left with this portrayal of Avery. Just curious, did the real Avery speak 25 words a second?