You need to add new collector after grand total one (Mage_Sales_Model_Quote_Address_Total_Grand). It has to modify sum that was set by grand total collector.
I spoke about such a case at MageConf conference in Ukraine week ago. Video and slides are not available yet, but you can download demo-module that was described at conference. There is an example of total collector that calculates wrapping price.
You can modify my demo total collector so it'll be inserted in collecting process AFTER Grand total collector (see config.xml in module etc directory - remove <before>subtotal</before>
node then use <after>grand_total</after>
instead) and modify collect() method just to set grand totals to your predefined values:
$address->setGrandTotal($someValue);
$address->setBaseGrandTotal($someBaseValue);
Or you can leave this module as it is, but set negative totals in it. So Grand total collector will subtract them and lower grand total value as you wish. Also in such a case customer will be able to see your negative values (give them in fetch() method) and understand why grand totals were lowered.
Have fun :)
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