You say that like it's just a fact to be accepted, but they didn't really explain that and they showed Bev going to put the poison back in the closet right after which is a pretty strong implication. It's not cut-and-dried that way either, but that's the whole point of the conversation earlier - it's an open end for the viewer to try and close however your mind closes it (unless the writer chimes in officially or something)
Edit: I'm finding out that ScreenRant really loved this show now lol. Here's their case against Bev, stating she could very well be who killed him. Here's the final paragraph:
This does not work in the favor of Bev Keane, who has essentially had free rein to do as she likes in the name of the church for decades before the arrival of this much-loved priest drew new attention to her cozy setup. Thus Bev takes drastic action and poisons the priest throughout the episode, likely by tampering with his food and drink. Early in the episode, when he first falls ill, Bev can be seen bringing Paul a glass of water. Later on, episode 3 of Midnight Mass makes a point of showing a handyman fixing the water supply into the priest’s small house at Bev’s behest—likely because she has been adding rat poison to the tap for days, gradually weakening the priest in the process. Thus the biggest unsolved of Midnight Mass may have an answer after all, provided viewers are willing to do a little digging and invest time in a rewatch.
Look, I don't blame you for getting confused because I was also a bit confused at first exactly because of that poison scene, but I realized that it didn't make sense and the intention behind that scene was just to remind you the poison is a thing. Imo they shouldn't have included that scene because it was unnecessary and confusing. Also the fact that Pruitt's and the dog's deaths were similar when they were actually unrelated. Screenrant is also wrong, here is why:
1) I thought of the idea that Bev would kill him to have free rein, but that doesn't really make sense because Father Paul and his miracles being around seemed to work largely in favor of her, since it made so many more people want to go to church. You also have to consider that at that point she probably knew it was Pruitt already, since she was shown looking at the newspaper photograph. And also it would be incredibly reckless to poison him with the poison she was already being suspected of using earlier on.
2) If he had been poisoned, Pruitt would suspect her. But he never said anything indicating he suspected he had been poisoned or anything like that. He didn't even question why he died at any point, as if it didn't seem weird to him.
3) There's no clear reason why she'd gradually poison him if she was going to give him a strong dose and kill him eventually regardless. If anything it was dangerous since it could possibly make him suspect things or run medical tests.
4) Pruitt went to the doctor. The doctor didn't say anything about being poisoned, she told him it's like his body is fighting off a virus. This is a clear allusion to the vampire blood, which she also described as possibly some kind of virus, the concentration of which slowly increases within your blood. The doctor's explanation also indicates why his eyes were bloodshot when he died.
5) Why the dog poisoning scene? That was just so that it could be more clearly conveyed what kind of person Bev is, and also so that the viewers are introduced to the poison. It wasn't intended to make you think Bev poisoned Pruitt in a similar manner. Also Bev looked far more surprised at Pruitt dying than she was when the dog died.
6) Pruitt is shown retching and coughing up blood at numerous times which don't seem connected to him having eaten or drunk anything.
7) The vampire blood essentially being a poison in reality instead of a solution ties in very well with the theme of alcoholism. At numerous points parallels are made, for instance Pruitt being caught with the flask/drinking what was assumed by others to be wine, telling Joe he knows what his compulsion to drink feels like, the audience is reminded that the Muslim character can't drink alcohol and he does not participate in the mass, the recovering alcoholic also avoids mass, the pregnant woman "miscarries" etc. The vampire blood is alcohol, and it is what poisons Pruitt.
At this point I am 100% certain there was no intention to make Bev seem like she poisoned him, the shot of her putting back the poison was just misplaced and they didn't realize it could confuse the audience.