Ben,
Consider "firing" the clay (a.k.a. calcination) before the electron probe. Do this in a TGA to get a very accurate determination of molecular water (<200C), organics ~250, various OH groups 250-500C, and carbonates >500C. Then 'probe away on the anhydrous product, which will polish better and is more beam stable.
Depending on the alkali content of your clay, it may be feasible to sinter or melt the TGA product. Melting is advantageous if your "clay" turns out to be a heterogeneous mix of minerals.
Good luck,
Jared