For me the taxes should be on the same group as a group represents a kind of taxes (sales, purhcases, service sales, etc). This makes it easy to create a tax rule that substitutes each kind of taxes for the diferent parties or suppliers.
Having said that I think you should fix the problem by adding a check on Taxes to allow to exclude them from tax basis. Then you should override this method to return false for Imports and EU acquisitions.
This will allow you to compute the values from normal tax groups on cash basis and exclude the required one.