I suspect the main reason behind the need for harvesting at night is that the demand exceeds the supply for super high density harvesting service, and contractors harvest day and night in order to face the demand.
As soon as there are enough providers, working extra hours will become less interesting and this kind of practice will go away. This kind of harvesting is a lot quicker than previous practices, so harvesting during the day will be more than enough.
Harvesting is done usually in the winter (ranging from November to January) so only non-migratory birds are afected, and even then only those nesting in super high density orchards.
The harvesters are quite expensive, and usually only larger producers own them. This kind of investment is tricky, because for the most part of the year there is nothing to harvest (although there are some other crops where the harvesters are being tried in order to recover the investment more quickly).
Of course no farmer wants to needlessly kill harmless birds, but I will wait for more data, since there has been some hype regarding super high density orchards in the past months, usually portraying them as something horrible and bad to the environment.
By the way, birds to not get into the oil presses, because olives pass through a mesh in order to remove branches and leaves. Then they're washed, so there is no risk of contamination with dead birds.
I also suspect the decline of bird populations in the south has something to do with the big fires of past years, that forced northern predatory birds to come searching for food at lower latitudes. I have never seen so many eagles like this year.
Or the other side, the Eurasian magpie populations seem to be doing fine, as well as the once endangered storks.
Edit to add: the research cited in the article is not research but an information notice by the Environment Council of the government of Andalucia.