When you use the AE 3D Camera Tracker, you also get Orientation info on the X,Y & Z Axis. SkyBox Composer can use this information to stabilize your 360 footage. This process is done with a couple of clicks as demonstrated by Charles Yeager in this tutorial on 360 Stabilization.
Once you have stabilized your footage you can easily straighten the horizon with the SkyBox Master Camera Z rotation Controls.
Charles Yeager is a Filmmaker & Motion Graphics Artist currently residing in Arkansas. His projects have been recognized by Canon, Video Copilot, Vimeo, Filmmaker IQ, No Film School, Film Convert, BOOM Library & Filminute. See his portfolio at yeagerfilm.com.