Ivy League schools are probably skeptical of a kid who’s been homeschooled, has some very suspect biology courses, and writes one of his/her essays about picketing the funeral of a gay soldier. These kids are about 0.01% of the Christian population.
Similarly, I doubt they’re favorably inclined towards those whose essays discuss religion in a way that implies Christianity is superior to other faiths. I’m reasonably certain 0.01% of Ivy League applicants actually write anything of the sort.
The 99.98% of Christians who belong to neither group aren’t likely to face religious discrimination. A substantially larger percentage than either of the above groups seems to believe they’re a persecuted minority. It’s hard to defend your faith when you represent a mere 70% of the population.
As a card-carrying member of the Liberal Conspiracy to End Religion, I can assure you that the last thing we want is to prevent Christians from attending our Reeducation Centers (also known as the Ivy League).