Yup, I know those instructions. But I hoped the custom scenario was offering a lazy way to do this and I just was doing some mistake
Like it or not, that's the only way to change the game options (as far as I know) after creating the game in Custom Game.
First create a WorldbuilderSave file by, as the name would suggest, saving while in worldbuilder. Then, if your computer uses Windows (or I assume that's the requirement) go to \\archive\users\*your username here*\home\My Games\Sid Meier's Civilization 4\PublicMaps (at least, that's how its set up on my computer) and it should be there.
You could edit it with notepad and add in "Option=GAMEOPTION_NO_GOODY_HUTS" between the "calendar=" line and the "victory=" lines, up near the top. Although, I believe that's only a game option in BTS.
If you wanted to completely restart the map without huts, then you'll need to copy and paste all the data to another notepad or notepad++ file, change the number of turns and techs to their original state:
Era=ERA_ANCIENT
Calendar=CALENDAR_DEFAULT
GameTurn=0
StartYear=-4000
You may also need to go through the plot data to find any plots that include having a city built on it and delete them.
Although, you should probably not listen to me, because I can't get my own scenarios to work, but that is how you can edit your maps.