of course the warnings about oakland from outsiders are a tad ridiculous. you're not going to get shot at in jack london square, especially near the jack london inn. if you really need to not go to oakland there are two hotels in emeryville within walking distance from the station, one is literally on the other side of the tracks over the footbridge. you can also disembark in richmond and get on BART and go to berkeley or wherever else would be "safer"
Well - I was walking down the street about a block away from Jack London Inn when I saw someone pull out a gun. It wasn't displayed in anger or anything. I think it was just someone showing it off to his buddies. I just put my head down and walked away.
However, it's not as if it would be easy to keep dangerous people out of a public place without some sort of perimeter and security checks (like I saw at one of the Super Bowl 50 events). The movie theater there always has an armed security guard now, although I see that at a lot of movie theaters now. I remember when there was a shooting outside of the theater. For several months Oakland PD would station an officer in a patrol car while the theater was open.
For the most part the kind of violence around there is targeted gang activity. I've never felt particularly unsafe around the train station.
As far as Jack London Inn goes, it's not known for being so great.
Maybe the Waterfront Hotel?