I haven't tried this myself but one option is to manually delete them. Go into the Saved Variables folder and use a program like Notepad to open the relevant file/s and delete any mention of the guilds.

I found guilds mentioned in ArkadiusTradeToolsSales.lua where you'd need to delete this section:
["Guild Name"] =
{
["keepSalesForDays"] = 30,
},

I don't think anything would go wrong as a result of doing that, but it might be a good idea to backup the file first just in case.

I've also got 15 ArkadiusTradeToolsSalesDataXX.lua files and they mention guild names, but that seems to be records of individual items sold, so if you never used their store the guild shouldn't be mentioned in them.

I found the file and deleted those lines but the guild is still listed in my settings. I relogged twice but no change. I may just uninstall and reinstall and hope that gets rid of it.

It's weird because I never sold a thing in that guild store.

If you manually change SV files you must logout before! Else the data will be restored after a reloadui from ingame memory stored tables.

Minion SV delete is Btw the same as logout and delete the files of the addon in folder live/SavedVariables

In ATT add-on settings you can set the retention for the Guild to 1 day, then wait few days and it will be gone from the ATT GUI