Why do some Atheists say Christianity is harmful?
Because it is. Most of the reasons why derive in some way from its self-given right to presume what other people ought to value and believe in.
Obviously not all Atheists claim this, most atheists dont really care about ones faith. However there are some atheists who claim Christianity is harmful as a religion. They tend to be more on the antitheist side.
True enough.
My question is why? And how? How is christianity in any way form or shape harmful? Some say its because of the strict rules, but how is that bad? How are rules who lead to a better society bad?
Yes, that is one of the causes of harm. The promotion of theocentric deontology as if a source of morality it were; worse still, as if it were the one and only.
In truth, deontology is at best a poor substitute for ethics.
And how is sexual purity exactly a bad thing? I dont see how Christianity can be harmful at all. So why do they claim it?
Branding denial of carnal desires "purity" is presuming to know what is best for people in general. That is just wrong.