Their natural teleportation could perhaps be limited to places where the individual has been to or has seen before. So each individual probably can't teleport anywhere in the world because, well, it's unlikely one person visited the entire planet.
The interesting thing about this concept is that it also explains why this species doesn't seem to be space-faring. They've never felt the need to be. I wouldn't be surprised if they've never even developed modes of ground transportation like cars or, well, maybe not even the wheel. Because, well, why would they? They can just teleport wherever they want to. This lack of transportation technology, however, binds them to their home planet. If they've never been to or seen another planet, then they don't have the technology required to get them there in the first place.
If the limit is defined as "places they've seen", then the planet should probably be moonless, otherwise they'll have tried teleporting there at some point in their history. But even if there is a moon, that's just one more place where you need to control them. My solution below is scalable, so that's not much of a problem.
Notice that I described this as "their natural teleportation". One might say that such a limit would also make the species useless as engines for FTL, but that's not necessarily the case. By studying the species (perhaps some cadavers), your scientists have been able to develop technology which would harness the species' ability without the "places you've been to/seen" limit. Put the specimen in an induced coma, put it in this special tube, place some uncomfortable probes, and your ships can now teleport across the galaxy. Should the specimen somehow escape, that's unfortunate and your ship will be stranded. But the specimen will still be bound by its own limits - the technology you developed only works for your ships, the individual fueling it has not been "upgraded" in any way. And since the only place they know is their home planet, they'll just teleport there, where they'll still be well within the confines of my solution.
So, now for the actual solution:
Firstly, you study the species. Find out how they reproduce, how they raise their young, how they teach them to teleport (even better if it's not a learned skill, but a natural one). Once you are confident you'd be able to breed and raise a newborn into adulthood, move on to the next step.
Now, you annihilate the entire species (so much for "willing to kill a few hundred of them"). Or, well, almost. Kill every single post-pubescent member of the species. And I mean all of them. If you can develop some virus/poison/nanoweapon which accumulates over time but can then be triggered to kill all the adults at once (they're peaceful, so begin by trading with them until you're confident you can trigger the hidden bioweapons in such a way as to kill all adults), that's probably a safer bet than trying to kill them by arms (wherein some might figure out ways and places to hide), but whatever floats your boat.
Now all you have left are a bunch of kids. These are young and can't survive without their parents. They've also not had time to discover vast regions of the planet, so their teleportation won't get them very far.
And then you start building your farms: opaque domes all over the planet. Move the kids into these domes. Once they're in (they might even come voluntarily: remember, they're kids without parents, they're probably starving and will accept any lie you tell them about food), immediately place them into induced comas. Once they've past puberty, start breeding to create the next generation. Once they've bred sufficiently, ship them off and start fueling your first spaceships. (Or, if you fear the risk of escape, simply kill this generation off. After all, they'll be the last generation capable of teleporting out of your domes. This just means you'll need to be a bit patient before you can start using FTL. But then again, your empire's probably existed for centuries or millennia. What's another twenty years?)
Now you have the second generation of infants.
If teleportation is a natural (unlearned) skill, there's no need for them to ever be conscious: immediately place them in induced comas and wait until they mature.
If teleportation is a learned skill, that's why you learned how to raise them before you began, and why the domes are opaque. Create nurseries inside the domes where you teach the kids to teleport from one side of a room to another. They'll never leave the domes and they'll never see outside. The inside of that dome will be their world. They won't know there's anything out of that dome to teleport to - which means they won't even want to - and even if they did, well, they haven't seen or been outside, so they won't be able to.
Once this second generation comes into puberty, have a big party with cake. The cake is laced with coma-inducing drugs. Once everyone's passed out, into the farm they go: breed the third generation and then plug the second one into your ships.
Rinse and repeat.