Open the client and put teh same in TEST mode.
First delete all the transaction data in GL,AP and AR.
Secondly delete the master data if it is not shared or required for other company codes.
Reset the Company code in Asset Accounting (this will delete both Master and Trans data in AA)
Now go to EC01 and delete the Company code.
Go to SE16 and check if company code is still available in T001 for confirmation.
Note : 1. Please check with other module experts if they have concerns, if any.
2. This methodology suites where CO is not set for cross company codes.