I've also seen the film theatrically, and those halos are definitely in the photography and on the film itself.
At the risk of digging up a deceased thread, I'd point out that, back when I was in film school, Days of Heaven
was one of my favorite films, and I watched it as often and as obsessively as many of my contemporaries did with a very-different work, released the previous year, that was set long ago in a galaxy far, far away. As such, I think I'm intimately familiar with the imagery in early-generation prints, and I never saw halos as pronounced as they are on this BD.
Another curious point in this "director-approved transfer" is that the end titles are in white text on black background. This is most definitely not
as it was in the original theatrical release, where the text was canary yellow on black. (The Paramount DVD had colored text, but the yellow had aged to a burnt orange.) Not a big deal, but I wonder why Malick decided such a minor change was needed.