I would go for:
1) use their preferences and experiences (pretend you don’t know what you personally want)
2) imagine you knew everything you could about the impacts.
Which I think is considered the standard approach when thinking behind a veil.
As you say, you might find it hard to do 1) properly, but I think that effect is small in the scheme of things. It’s also better than not trying at all!
“This suggests that, behind a veil of ignorance where self-interest is not at play, those at risk of malaria but not worms might regard treating worms as most important and those at risk of worms but not malaria would treat malaria.”
Wouldn’t they then cancel out if you took the average of the two when deciding?