I'm guessing that it goes something like this (No spoilers, just conjecture):
Hooded Guy faction starts tainting the crops, starting with the more remote areas. The sacred deer, protecting the people, eat the crops to stop the people getting ill. Tainting the crops slowly moved in, towards the capital. Deer keep eating tainted crops as a protection measure.
Hooded Guy shows up openly at some stage as an "expert" to try and "combat the problem". Really he's a wolf in sheeps clothing and is the cause, or near the cause, of the actual problem. The only "safe" field of crops is being fed to the Royals and Co. causing many of them to get sick (like the King, he's getting poisoned, cause the crops he's eating are tainted).
The MC shows up and does his barrier thing, aimed at keeping those with "malicious intent" out. The deer walk through it like it's not there, because they don't have malicious intent, they're trying to protect people by dealing with the corruption.
Hooded Guy convinces desperate people in power to cull/kill the deer, leading to the blessing going away, leading to...something? I was going to say leading to the kingdom being conquered, but they're already weak and vulnerable, so maybe a more quiet takeover? or as part of some wider conspiracy against sacred beasts or for some evil god or something? I dunno. ...leading to 'bad outcome' I guess.
WHY the sacred beast god spirit deer thing can't communicate the danger in a more direct method is unknown. But I guess if that happened, we wouldn't be getting this story arc.