This is indeed the way it was intended. I don't think there is a way to do this in default OpenERP. You could invoice the whole and subtract 50% manually, but of course this would defeat the purpose.

If the invoice only consist of 1 product you could alternatively select a product in the wizard that you run to invoice a percentage. The selected product will then be used on the draft invoice and it does have the right amount of tax as well as the right account.