Pretty much what D9's said. This isn't The Tudors (or a historical costume drama based on actual history). there's no point in trying to look too deep into the historical accuracy. Castlevania has always been anachronistic and fantastical. As he's already said, we already have a case of here, there's a super powerful vampire called Vlad Dracula Tepes, who's a bit of a scientist and occultist, and has a history of impaling people, but he's not Vlad III Dracula, Voivode of Wallachia. Yeah, the church was made possily a smidge too antagonistic, from a storytelling perspective and a limited run time, I can tell why they chose to make them the focused bad guys for the season, especialy after spending time showing that Dracula had valid motivations for getting so upset over Lisa's death. Plus, it's Warren Ellis writing, and he has cerain very strng views on things, and it shows in his work. I get why some people are upset over how the church is being portrayed in this - from both the canon to the games perspective, and from the perspective of hey, the church is getting shown in a really bad light here (which is potentially harder to not get upset about). Maybe taking a short step away from the keyboard might be an idea before it descends too far into an arguement. We need to remember that this series is historicalesque fantasy, it's not shackled to historical accuracy, just as it's not shackled to telling exactly the same story as in the games - heck, even the games' makers at times brought their own takes, and there was a serious lack of continuity until Iga came along and tried to put one together. From a writer's perspective, I can see why they chose some of the directions they took - I have a few friends who are authors, and have chatted with them about it.
I made my peace ages ago, both when Warren Ellis was posting about the project originally, and when Adi Shankar announced he was getting a series made, that it wouldn't be coompletely faithful to the games, that it would have its own continuity, and do its own thing. To be honest, I don't mind this. I feel like a fresh breath of life has been given to the series, especially now, when there's been so little come out aside for gambling games. It goes back to the original timeline of the games. It's got its own character, and that can give it space to grow and develop, and it can bring something a bit new to the table.
On a side note to Shiroi: I noticed that as well! I'm getting a feeling that quite a fair bit was held back, not everything was told about Lisa and Vlad's history, so as to keep Alucard a secret for the big reveal. Also storytelling-wise, it's better to not tell everything at once. Hopefully we will see more in season 2.