Okay, so I've had the DLC bug for at least 2 weeks now. At first, I just set the game aside and waited for a patch. Still waiting, obviously, I decided to try and play last night. Instead of carrying on the "Come fly with me" quest, I simply went on to another quest (Helios). I deleted all of my corrupt saves, and believe it or not, the game is working fine now. So apparently you can just avoid the glitched quests (unless of course you're locked in a building or something). I saved often, and now all of my saves are working fine. So, if at all possible, just avoid the bugged quests, and you should be fine, simply return to them once the patch is out.

Well I deleted the DLC from my hard drive and started a new game had no problems completing come fly with me. I've also had no problems in vaults. I make a semi- permanent save before entering any building, then make another semi- permanent save before each loading zone within a building.. and also before I speak to a main character.. Once I'm out of the area I'll play for a few more hours or days, depending... before I delete those saves.
Deleting the DLC and then loading an old game will work fine.. (your dlc stuff just disappears.) But I wasn't sure if it would actually remain glitched or not so I deleted all previous saves, cleared the cache and started a new game. Seems to have worked. Granted I didn't have any big bugs when I had the DLC..I just heard about it and decided it was better than risking it. I was only about 30 hours in and wasn't happy with my character build anyway. Now I'm over 150 hours in and have had no major bugs whatsoever.