You'd need to have a contra-rotating counterweight to stop the ship from trying to de-spin the arms by rotating the hull in the opposite direction. If the ship is big enough you can have two sets of arms, or rings, rotating in opposite directions. Otherwise just a really heavy flywheel will do it.
The spin mechanism also means the ship will resist course changes, as the gyroscopic action of the arms will tend to try and dampen down any changes to the rotational vectors of the rings/pods.
During combat, when you might need to change course a lot, you'd probably de-spin and lock the arms/rings in place.
The pods can also be designed as lifeboats, with low berths or emergency shelters in them. Give them a fraction of the power plant and lfe support to represent independant systems.
Another system is to couple two ships together with a tunnel or cable and spin the whole ship in pairs around a common centre.