Actually, the HSCS-2 femtomachines, the way I see it, if anything, are proof that the concept can work, rather than a counterargument. Assuming the HSCS-2 could stop this stuff even in concept. there are three reasons why that isn't good enough to render Grey Goo useless.
1. HSCS-2 is used exclusively by SAY ships, which means planets and non-SAY vessels are still nanophage food.
2. HSCS-2 femtomachines only affect organic material, and most of the nanophages (IE the original nanophages, and the nanophages created by the consumption of hull and structural material, etc. rather than crew or organic components) are of inorganic composition, unless the targeted vessel is a bioship. Also, the first nanobots to come into contact with the HSCS-2 fluid will usually be the ones created by the consumption of the lining of the HSCS-2 conduits, which (I hope, for SAY's sake) is not able to be dissolved by the HSCS-2 femtomachines.
3. Nanophages can always be replaced by femtophages or whatever prefix is necessary, without changing the general concept of the Grey Goo weeapon
If the general consensus is that HSCS-2 would, in fact, somehow stop this stuff dead in its tracks, then perhaps it could be that SARA invented this stuff for the same pruported reason the Koqui Armed Forces use poison gas grenades - "Were immune, so let's take advantage of those who aren't".