If you've got Translocators, you should be able to automate this fairly conveniently. Rather than regulating the amount of emerald in the smeltery to ensure there's always enough to melt down the next villager, you could go back to your first idea and toss some iron or something (might be better to use tin or something else that can't make pig iron) in there. A pair of fluid translocators with redstone upgrades (if you click the button in the middle of one, but not the other) will transfer fluids from one tank to another when given a redstone signal, and from the second tank back into the first when the signal is turned off. If you attach one of these to a smeltery drain, configure it to only accept molten iron (you can do that with fluid translocators, right?), and attach the other translocator to a tank (a Buildcraft tank or any of TiCo's seared glass-type blocks will do), you can transfer the molten iron out of the smeltery and back at the flick of a lever. Connect it to a redstone clock of some sort and voila, automation. Every few seconds, if the molten iron is on the bottom of the smeltery, the translocators will pull it out and then put it back in. If there's any molten emerald in the smeltery at that time, the iron will then wind up on top of it.
You will, of course, want another output from the smeltery, filtered to only extract molten emerald.