I will try to answer your question, I hope you find it useful.
Your actual question is "how to handle these questions". Questions where your actions turn a less-than-optimal situation into another less-than-optimal situation.
So, the answer, is a process of how to handle them:
1) Question the numbers you are given, be it statistics or raw data. Who is saying that there are 0.1 expected deaths a year for the plant? How do they figure that? Who is saying that the local population can expect 50 deaths per year? Did they figure that correctly?
2) Question the motives behind the people giving you the information. Is the same person giving you both the plant and population death estimates, or are they two different sources? What ulterior motives might they have in selling the story in a particular way? Do they have something to gain or lose other than purely the human losses?
3) If you decide you can trust either the new numbers or the old ones, then do the math. For this example let's assume that the numbers are right just so we can continue the discussion. "0.1 deaths/year" doesn't help anything, convert it: it's 1 death per decade stacked against 500 per decade. Now we get a real sense of contrast.
4) Consider what is likely to happen in each scenario. If you don't build it, and nobody else does either, 500 per decade will die indirectly because of you. If you build it, one person per decade will die indirectly because of you.
5) Consider whether the units are the same. In this example they are all human lives. However, one side has willing and informed employees working in a dangerous plant dying in order to provide clean water for their community; the other side has regular citizens and children unwittingly dying just by drinking water.
6) Additional considerations: workers can try to make it safer to work there and be extra careful, aided by practice and handed-down experiences. The general population cannot stop drinking water.
7) Finally, having a much stronger grasp of the situation, question the entire thing. Let's look into the situation. Why do they want to build a plant? Because the water is killing people. So the actual core problem is not the plant at all, but "why is the water killing people?" Is the community uneducated in disease control? Is waste being mixed with the drinking water due to negligence, ignorance, or otherwise? Would the community benefit more from the building of much cheaper facilities such as latrines to keep the water from getting dirty in the first place? We could learn that it's as simple as human waste being deposited somewhere and then having flies going from that place to where they keep their drinking water; in which case a 30 minute class a cheap plastic lid to go on top of water wells would be infinitely cheaper, faster, and less deadly than building a plant. It definitely merits an investigation before assuming anything.
I hope this helps your journey.