Unfortunately, the concept of economy is deeply part of the core of Nations. Changing it so it could not depend on an economy plugin anymore would be a huge task.
However I see here a trick that could emulate this sort of feature, but I'm still not sure about what you exactly want. An acceptable idea would be to change the plugin so when it has to perform a transaction, if price is set to 0, it doesn't query the economy API. But that would mean setting all prices to 0, including nation creation price, taxes, upkeeps etc. And I'm not sure it's what you want. Is it ?