When I first came to Junktown, I thought I was supposed to kill a rabid dog, so I
did. Now that I learned he could be tamed, I tried to back up, but he seems to
be permanently gone. I even restarted from Shady Sands before I ever
even stepped foot in Junktown, but no dog and the man still thanks me for
helping him.
Any ideas? Do I have to back up before hearing of Junktown or something?

That's ridiculous, I don't even think a bug like that is possible. Try just making a new game..

Whoa, thats bad.
Other than completely starting afresh, I can't suggest anything else.

(south park mode) You killed dogmeat? YOU BASTARD!!!!
That is very odd, think a restart is in order.

Save game sounds corrupt. Restart with a new game.
(It should not take long to quickly get to this point)

Poor Dogmeat! I can't believe you shot him! He's not a bad dog, he's just misunderstood. All he needs is a snack or an owner with a cool leather jacket...
These problems wouldn't happen if he could talk like the dog in the old Don Johnson Post-Apocalypse movie (mid-70's). Anyone remember that one? Freakin' hilarious, but dark.

Maybe start a new game and _then_ load your last savegame before you killed Dogmeat.
I had a different bug, but maybe with a similiar cause: When I went to the Gun Runners, I told the guard I needed to talk to Gabriel, so he let me pass and didn't walk back to his original position, guarding the bridge. But whenever I loaded the savegame - at which point he still didn't go back to guarding the bridge - he just stood there again. I may be very wrong, but my guess is, that the guard's position isn't saved with the savegame.
So maybe the reason is the same with the "Dogmeat quest": Its status isn't saved, so whenever you load from a point at which he is already dead, he stays dead, whereas when you load from a point at which he's still alive, he stays alive.

A Boy and his Dog! Man, I haven't thought about that movie for years