You are able to delete a payment from TM3 however it is important to note that you can only delete a payment which is unreconciled. If invoices are reconciled against the payment you want to delete then you should unreconcile these otherwise your finances will completely mess up.
At the top right of the payment there is a more button. This is highlighted in red in the image below.
When you click on More it brings up the options below. You should click on Delete.
Once you click on Delete a confirmation box will appear and you should click yes to delete or no to cancel.