It's not the fact that it changes them, it's the thematics that goes with that.
The impregnation of a woman by a Genestealer (the sexual abuse) eventually leads to them becoming their slaves and servants (and this is due to telepathic control and links to the child, it's not even 100%, as it's not fleshed out - the mothers are still human). They've a maternal instinct for their inhuman children, amplified by psychic juju. When impregnated, they go about their lives, not even remembering the Genestealer's Kiss. They don't instantly turn into aliens or zombies. They're women that have, somehow, become pregnant, and carry on with their regular lives, and want to guard their babies.
These abused sexual victims, who are then killed for being abused could be seen as having far too many real life parallels. Add in the fact that, at no point (unlike how mutants and psykers are dealt with), are any individuals executing them seen as unfair.
Edit: Different sources have different degrees of control and change placed on the victims, yeah. But still, the thematics is difficult and extremely horrifying (burn the **** victims! Sexual purity above all!).
Edited by bluntpencil2001