To reset a company in a multiplayer game through the console you need to use the "reset_company" command.
When you type reset_company <company-id> at the console the company using <company-id> will be deleted with all its stations and vehicles.
To find out the id of a company to clean, you can use the "players" command which will show all companies on the server and their associated id.
If you are playing as a client on your own dedicated server and want to use this command you might want to look into the rcon command.
Also see a detailed list of all console commands available and their usage.