I don't think you need a mod really. I'm fairly certain you just made a mistake and didn't turn them off when you generated the map. It happens, it's no big deal. And you should only have to turn off ruins at the point when you actually generate the map. Once you modify the map with common starting points and go back and start the game up it shuldn't matter wheter you have them turned off or not. The game shouldn't add them in at that point if they weren't in there at map generation.
If you did want to make a mod to turn off ruins, you wouldn't need to set the mod up on PBW. You use the mod to generate map files and then use them in the stock game. The only time ruins are assigned to a map is when it's created. Even if you did want to be doubly sure and start the first turn using the mod, I don't think the players would need the mod. The balance mod that I made modifies the system type files which are used at map generating time and the players don't need the mod to play their first turn.
In fact if you only change the files that control the chance for ruins to appear, the players may not need the mod at all. The balance mod I mad tweaks those system type files that are used for map generation and the players don't need to use it for their first turns, even when it's used to actually create the first turn. Hmmm, maybe I should just tweak out the ruins in the balance mod.
You don't need to turn off the unique techs. That would change the components file and make a mod that the players and PBW would have to have, but it's unneccesary. Without ruins there is no way to get those techs anyway.