I would hazard a guess that we know Ebola to be pretty close to 100% lethal, and if you know that three out of three control animals died, then the virus is "working" and there's no need to sacrifice many more animals.

Exactly. The control group is there to, for example, make sure your culture of Ebola is really that, viable and so on. If they didn't get sick, let alone die, you'd know your experimental group results were invalid.

Monkeys are also very expensive animals to do research on, and no one likes to kill them, or at least we don't tend to have the same sentiments about mice and rats.

It looks like the 18 animals were actually sub-divided into at least three test groups. One test group got the drug after 3 days after exposure, one at 4 days and one at 5 days. So the number of animals in each sub-group is closer to the control.

It wouldn't surprise me if there were actually six test groups of three animals each (perhaps divided by both day-of-treatment and something else like drug amount), thus matching the control. But the article doesn't actually imply that.