Excellent point!
Especially if we consider the layman’s definition of what health is: “being free from illness or injury”. This definition opens up the promotion of health to the same kind of objections that fells Negative Utilitarianism, namely: if all that mattered was reducing suffering, isn’t the easiest way to do so merely getting rid of all the sentient beings?
We should be open to the possibility that making the world less ill might also make it worse off, if there was also a simultaneous loss of those other things of value besides health that offset the reduction of illness.
We should be clear that when we focus on QALY’s it is only because it (arguably) is one of the most tractable ways of promoting well-being.
The Global Challenges Foundation has recently launched an essay competition with a $5 million prize (!) awarded to the best ideas for new forms of global decision-making. The foundation has previously funded work on global catastrophic risks, so I guess they would not be opposed to an EA mindset.
More information is available at their homepage.