It's interesting that they could ask for a (GST-inclusive) residual (or "balloon") payment, when the contract was drawn up pre-GST.
Apart from consulting the ATO and your accountant, you may also wish to "carefully" peruse the wording of the contract, esp. as relates to the balloon payment...If it doesn't mention a "service" fee, you *may* have a leg to stand on. Again, however, check with the ATO, as it (the GST) may be applied retrospectively...
PS. The usual disclaimers apply re: advice and all that...