I have no desire to perform eugenic experiments on my dwarves, so the false positives are the only aspect of the anti-eugenics system that will really affect me.
I like the idea of Urist McConspiracy deciding that the man is keeping him down, even when the deaths in question really are accidental.
True, we don't want to totally screw over the player, whenever a string of unusual deaths occurs, but if the penalties started out small, and then got more serious the longer the streak got, I think it could make for Fun politics, that are at least deeper than the current system, of nobles demanding random things, to simulate a demand for luxury goods.
It could start with a simple bad thought, about how hard his people are getting hit lately, and get progressively worse as the trend goes on. You could get a swarm of like immigrants, trying to support the ailing community, or immigrants like that could start avoiding your fortress, or eventually, you might even get sieged by some faction, that is opposed to eugenic culling. --all without necessarily being responsible.
Likewise, a simple streak counter isn't going to do it. It's far too easy for an actual eugenicist to hide his motives from something like that.
Dwarves should look at the last X deaths, (depending on their paranoia levels or whatever) and if the percentage of dwarves like himself if notably higher than the percentage of like dwarves in the fort, he should start to get worried.
To make these systems carry their weight, it might be cool to add in serial killers that pick their victims based on some trait pattern (the victims were all female blonds, etc.), which would have applications in dwarven crime mysteries as well.
Naturally, Urist McConspiracy is going to think the government is either behind the killings, or protecting the killer, for their own dark reasons. Google "Jack the Ripper Conspiracy Theory." Yeah.