I had a look at studies on flight crew mortality. The fact is that (so far) there does not seem to be any concrete evidence that the changes in pilot's working conditions are showing up in the mortality rates.
The good news is that (probably because of healthy cohort effects e.g. pilots are a healthier than average at the start) mortality rates are lower than the general population. The well known increase in skin cancer risk is one known factor. The other much more elevated risk is of dying in a plane accident. Given these are mainly when private flying there is a facetious argument that the harder we work and the less money we make the longer we will probably live as we wont have the time or money to indulge in this.
On a more serious note I did come across an interesting study of increased mortality in higher status jobs in Japan following the economic downturn. There is evidence that increased stress and work has had a slightly negative effect on mortality. Other factors for example being unemployed have a much stronger correlation with reduced life expectancy.
Overall I cannot (yet) see anything that would make the bean counters pay attention. I think the only hope is market forces (running out of pilots). Even there the situation only in the last few weeks does not look good with Transaero probably in trouble, Air France anouncing a long haul fleet reduction, Air Berlin and probably several also reducing their requirement for pilots.
I think a point will come where it is recognised that happy (and probably more healthy employees) are of benefit to airlines. Sadly I do not think we have reached that point yet with most of our employers. However a long term study focussing on Emirates and Ryanair would be most interesting. It is probably unlikely though to be supported by them.