To be honest, I think it's a reasonable motivation to encourage Network Rail to look into doing more to prevent railway suicides, especially in hotspots. As they have been doing. Not sure whether this is financially motivated on NR's part, motivated by the desire to avoid delays on the TOCs' part, or actually genuinely humanitarian. Probably a mix of three.
But whatever the underlying motivation, if these penalties in part cause NR (who, after all, really do have the responsibility here) to do more and therefore save lives, isn't that worth it? No matter how strange a system it might seem.
I agree that there will obviously be "false positives" — ones where NR pay up even when nothing could reasonably have been done. But given how much money is being pointlessly handed around anyway for various stupid reasons, I don't think this is a big problem.