A credit note will only be raised from a reject, if the order has already been invoiced. There is no way to prevent this. You will need to cancel the credit note instead.
Go to Sales
Click on Credit Note Menu
Select Credit Note Maintenance
Press Cancel C/Note
If you cannot cancel the Credit Note it is because it has been exported to a batch of invoices. If that is the case do the following:
Under the column 'Export to [Accounts Package]' there will be a batch number. Click on the number and it will open the batch.
Press F3 to delete the Credit Note from the batch. Note: You will need to delete the Credit Note from your equivalent accounting package as well.
You will now be able to cancel the Credit Note using the Cancel C/Note button
