Kischur Zelretch Schweinorg is a Dead Apostle because he fought Brunestud of the Crimson Moon who created the True Ancestors who in turn created the Dead Apostles.
Brunestud is the Ultimate one of The Moon and this one of the Aristoteles called Type-Moon. In the beginning over four thousand years ago he responded to a call from the collective will of the Earth, Gaia, to protect it from human corruption and in exchange Brunestud was allowed to live on the earth.
Brunestud created the True Ancestors based off his image as a natural protective system for the planet and to return it to it's natural state which is why Alaya does not act against them (remember that Alaya is the collective will of humanity which will deploy Counter Guardians to save humanity from destruction). after this he went around challenging other being on Earth and amassing followers in an attempt to eventually take the Earth as his own kingdom.
he eventually attracted the attention of Kischur Zelretch Schweinorg who was already a Sorcerer wielding the Second Magic. in a battle which Kiniko Nasu likes to keep to himself the 2 fought.
He was eventually defeated by Kischur Zelretch Schweinorg wielding Second Magic. He tried to pull the moon to collide with Earth but it was pushed back by Zelretch's magic, so it was unable to affect the planet. With all of his power, Brunestud did not foresee being defeated by a human, but lost to Zelretch due to being too late in understanding the power of Magic, "a rule outside of the rules." Before his defeat, he sucked Zelretch's blood converting him into a vampire.
Source: Crimson Moon - Profile - Background (2nd paragraph)
They're also generally hostile to both The Church and the Mage's Association. Furthermore, Dead Apostles in general have proven to be extremely antagonistic towards humans.
you are right that there is hostility it should be pointed out that the Association wont do anything unless the Dead Apostles risk exposing Magic to the public (as been their stance with their own Magi who can do the most inhuman thing so long as it's not publicly exposing magic) and given what's been happening with Aylesbury the Chruch, knowing full well what the Aylesbury Valesti is for, isn't going to make a movie
Due to the development being funded and developed entirely by human means, the Mage's Association and Church are unable to intervene until the advent of the ritual.
Source: The Twenty-seven Dead Apostle Ancestors - Attributes - Aylesbury Valesti (2nd Paragraph)
Obviously though when the ritual starts thew Church will probably get involved and if it's too public that's when the Association will get involved.
as for being antagonistic to humans, not entirely so. for the most part "human" in this case is anyone not either in the Church or a Magus. The Church hunts them down because they don't see them as Human and if they aren't human and can't be controlled they should be destroyed. Also within the 27 Dead Apostle Ancestors there are some who weren't even human to begin with and their origins explain why they would be against humans
Primate Murder is a Beast of Gaia and has the absolute authority to kill humans. it's counted as a Dead Apostle Ancestor because it's under Altrouge Brunestud's control and started to drink blood like it's mistress.
ORT is one of the Aristoteles like Brunestud of the Crimson Moon but he is Type-Mercury having crashed on Earth 5000 years before the Common Era in preparation for the event that would occur in Notes. it's counted in the number of the Dead Apostle Ancestors because it was discovered to have vampric abilities
though there are some Dead Apostle Ancestors who aren't our enemies in a way.
Merem Solomon was turned by Brunestud of the Crimson Moon himself back in the day yet he and Merem feels an immense sense of gratitude towards him since Brunestud actually helped him by turning him into a Dead Apostle, of which he has directed his gratitude towards his golden princess, Arcuied, since Brunestud destruction. also Merem like treasures and joined the Church to access their relics and became the fith out of eight executioner of the Burial Agency and thus hunts vampires. the Church knows he's a Dead Apostle however he is "a non-human who can be controlled", so to speak
Gransurg Blackmore was a Magus who fought and was defeated by Brunestud but survived. Brunestud made him his personal Magus and Gransurg became a Dead Apostle on his own though his magical research. after Brunestud's destruction he's worked with the Association like how Merem works with the Church though at one point the church had sealed him but we was able to escape. unlike Merem he only kills other Dead Apostles if they stray from the teachings or wishes of Brunestud.
while Dead Apostle Ancestors, Merem and Gransurg would oppose Altrouge who generally leads the rest. both worship Crimson Moon as a god and see Altrouge was an impostor and that Arcuied is the true reincarnation of Crimson Moon with Merem even helping her out at times (though Arcuied doesn't know how to respond to his unconditional affection). one of them even hates Altrouge for taking Arcuied's hair (i think Merem).
we also know that Kischur Zelretch Schweinorg is also Dead Apostle and he's willing to help out Magi having appeared during Rin Tohsaka's trail at the end of Heaven's Feel and created Magical Ruby and Saphire for Rin and Luvia.
As for Zelretch's allegiance, it's stated on the wikia that it's to humanity and the nearly extinct race of True Ancestors. while his friend Caubac Alcatraz is a Dead Apostle Ancestor (who like Gransurg became one though his own research rather than being turned) they were probably friends before hand and the 2 were at Arcuied's Coming of Age Ceremony (only Zelretch and Arcuied is shown).
Though whether he'll fight against Aylesbury Valesti is yet to be seen. his wiki page does state that he is
surprisingly meddlesome in worldly affairs
and given that in Fate/Extra the state of the world is suspected to have been the Aylesbury Valesti occurring earlier it might be bad enough for him to interfere. he could also just have the same sorta reason as Merem and Gransurg to fight it just because Altrouge is involved because he acts as a surrogate grandfather to Arcuied though it's not stated what his opinion on Altrouge is