When using the new call application from Android's Kitkat (v4.4.3 or higher) one can set SIP accounts over Settings > Call Settings > Accounts > Internet calling (SIP) accounts.

But how to delete an account if it's not needed any more? The delete button was quite frankly "hidden" since bright grey and white were used as colours.

Simply tap on the lower right corner and a button for removing the account will show up.