I killed Ullyses, and then nuked the Legion....thinking this would spare Ed-e. But I cannot leave the silo with Ed-e. As soon as I click on the elevator to leave, it tells me that I am losing his perk. I played on and searched all over for him afterwards with no luck.

How do I end the DLC AND get to keep Ed-E around?

I'm not sure, but I don't think you can keep him with you after the ending, even if he survives.

If he does survive, you should be allowed to find him again if you return to the area (and maybe even bump into old Ulysses again) ..,

As far as I know the Mojave ED-E remains unchanged, even if you sacrifice Divide ED-E.
The whole point in the sacrifice thing is to see if ED-E reaches Navarro, not really his existence.