I work in the area during the week at the local transit agency and my patrol area includes the area around OKJ. Sometimes I'll sit outside in my work vehicle for an hour or two monitoring our service. It really depends on your definition of a bad area. The area around the station is actually one of the better areas in the city. It used to be more industrial but many warehouses are now turning into Condo conversions that are rather pricy. Jack London Square is nearby as well which is a common gathering point for many. Upscale restaurants are starting to move in and change the scene. It really depends on your view of what is safe and what is not.
Driving through East Oakland I take reports on fights, robberies, and the like. It is just everyday life. Shootings are numerous but they tend to occur in East Oakland or West Oakland, not the area the station is currently in. With that said, no matter where you go or travel to across the country, there will be some element of crime, especially in larger areas like the Chicago's and New York's out there.
I would give the same advice for Oakland as I would give Pleasantville... Be aware of your surroundings, don't loiter around, don't display all your belongings such as your expensive phones as it makes one a target, and just use common sense.
With that said, Emeryville would be a better station to use if one is weary. The stations may only be 4 miles apart but they are in very different areas. Unfortunately, Oakland has a bad reputation when it comes to crime but hundreds of thousands of people are in Oakland every day without a problem. Just be street smart and the average person should not have a problem.