So I went to junk town and I was about to enter, when they started shooting me! So, naturally, I got upset and slaughtered everyone in town. OK, maybe I was irrational, but I didn't do TOO many groin shots - so you can say I went pretty easy on them.

Anyways, everyone's dead. Did I just ruin my game or can I truck on?

It should be fine. You don't need Junk Town to get the water chip, or to find where the Master is camped. You should try not to kill the Brotherhood though. They will help you out later on if you join then.

In my first game I slaughtered everyone in Junktown too. Don't worry, you'll be fine.

Might have some difficulty finding the next town, which I think someone at junktown could put on your map.
You'll likely find it on your own though, if you happen to go the right direction.

At least you should have plenty in the way of weapons, ammo and gear now...

Thats one of the things thats differs the game from most others
....you can just kill everything and still finish the game....you should
only first execute their quests and than execute them ;-)

Try to pay attention to what the guard said: holster your weapon(s) before entering the town, and don't proceed through the gate at night.

So in short, yes, you were irrational - you've already been asked to holster weapons before at Shady Sands (assuming you took the straight route to Vault 15 first).

Though if you prefer to just shoot your way through Fallout, you can.

I think Ian can also give you directions to The Hub if he is in your party. From the Hub, you can get directions to most of the other locations.