According to the patch notes for Destiny's latest update (Update 184.108.40.206), the final battle with Atheon has been patched so that players can no longer knock him off of his platform in order to beat the final battle and collect their reward. Also, Atheon will now be teleporting three random players through the timestream and no longer the three players furthest away from him. This will in turn make the encounter the way that Bungie intended it to be, and players will really have to work for the rewards they receive for completing it.
Beyond that the update claims to improve stability for all players, and said that they've narrowed down that issues for error codes "Zebra" and "Cockatoo" and now there will be different error codes based on a more precise issue. Now although they hoped to improve stability, post-patch I've personally been getting sent back to orbit much more frequently, with a message claiming connection issues (error codes "bee" and "fly"), and have also heard reports of other players having the same troubles. Hopefully we'll get a patch very soon that indeed does deal with these issues.