Yes, alchemy is a scientific approach to understanding "God's" creation. It is considered heresy by some because it isn't religious and incorporates some magic, which at that time in history is considered evil by the church even if it is holy magic. It is not evil, nor do I think that it is holy. It is simply a means of understanding the world and how things work. As for the vampire killer, it's referred to as forbidden because of its requirements. In my view, taking the life of another can't be seen as holy, even if the "victim" is willingly allowing them self to be killed. It's not easy taking a life and all life is sacred even the life of a monster like a vampire. The only reason vampires are killed is to protect innocent humans and killing someone or thing to protect innocent people is the only way to justify killing a living being. Vampires are beings of darkness who seem to hate Christianity and attack innocent humans. Thus, any weapon that can negate any special defense a vampire and is very effective against evil beings of darkness may in time be considered "holy" by people. If the vampire killer was indeed a holy whip, it would have been referred to such in its description in LoI. It's not though. Instead it is described as "a whip of forbidden secrets that is the bane of the children of the night." If you ask me, that description makes the whip sound anything except holy. The only reason the whip is considered holy is that it is effective against vampires and other beings of darkness and because virtually all the sub-weapons used by the Belmonts have at least some holy power. For example, in SotN, every time you attack an enemy with a sub-weapon, the enemy turns a little bright green indicating that the attack was at least partially holy. And it's just with the Belmonts. Even when Alucard uses a sub-weapon, it's partially holy.
In other words, the only reason the Belmonts are considered to have "holy power" is because they can effectively fight vampires and other evil beings of darkness are Christian and are completely human. At least, that is how I see everything. I could be wrong though.