We have the same scenario here in Brazil.
In Standard system, if you have the witholding tax code assigned to the vendor. The system will always calculate. So we have two options to avoid it:
1) Remove manually the tax code in MIRO (as you do today).
2) Develop in BADI MRM_WT_SPLIT_UPDATE (if the badi is already implemented by standard solution, you can do a implicit enhancement). So you can develop your own rule in BADI to remove the tax code when necessary.
Regards.
Gian