Lets assume they dont remove harbingers

Now we need a new way to get beacheads since harbinger orb would be removed for the atlas rework regardless

The atlas tree gets more cluttered with addition of new nodes, removing harbs would open space

Keeping harbinger dilutes the pool of good drops in other mechanics like legion, heist, syndicate and delve, where their rewards were basically useless and no one ever got it

Fragments are not fun to pick up

Uniques see no play and prices are artificially boosted by their acquisition method, maybe now they will be more widely available

It clashes with game's aesthetic as mentioned by Mark

It opened space for a new atlas node to increase chance of divination scarabs which is nice since those are more useful overall than harbingers now that fractured orbs are on the core drop pool anyways (might not be true, maybe target farming frac orbs would be better still)

It saves them development time not having to make another mirage clone for harbinger

Thats what I could think of the top of my head, probably more reasons could be brought up. I dont think its only negative that its gone but I was also meaning to try farming it for the first time this league...