I don’t think this problem is a show stopper because a non divisible fraction is still spendable to third parties (as a whole) or usable for put payments (by parts). It is like saying a bank note is a show stopper because it cannot be divided. And frankly we are talking about fractions of a safecoin that is currently valued 10 cents.
But if it is, then my proposal can be amended by limiting the possible factors for a division. Let us imagine for example that the maximum number of values in a MD is 256, then the vaults could control that a whole safecoin can only be divided in parts multiple of 1/16 safecoins and that such part can only be divided in sub parts multiple of 1/256 safecoins.
That way the lowest non divisible denomination is the same for everyone (1/256 safecoins).