Umm, the spine stayed stationary with respect to the planet on the background. So yes, it was spinning the opposite way to the bulk of the station. But only just enough to make it stationary.
Nothing wrong with that kind of an arrangement as such. Communications and weather satellites around Earth used to do it a lot, in the days when they were all spin-stabilized rather than held in the proper orientation by internal gyroscopes. They would have a cylinder body covered in solar cells, rotating enough to serve as a source of gyroscopic stability. And then they would have a little motor that would spin the antenna or camera cluster the other way, so that they would end up remaining stationary and pointing at Earth.
There would be no particular advantage gained from having the spine and reactor part of B5 spin in the opposite direction at a faster rate than the "just enough to cancel out movement" one we see. Indeed, the whole point of this counterspinning is to make the spine "immobile" so that it can receive zero-gee shipments and keep comm antennas and guns and sensors pointed at things and so forth.
Then again, B4 as seen in the time travel two-parter apparently had sections that spun against the habitat bulk at double the spin rate of this bulk, so effectively they spun in the opposite direction even with respect to the background. Hard to tell why. The two spins wouldn't "cancel out" any torque forces or anything. They'd just be a nuisance in the end.
Timo Saloniemi