OP asked about how to handle inquiries about this, not whether they should have done it to begin with. And what I'm asking is rather "why is this something that is an automatic red flag against them." I have seen the reasoning given for it, and imo it is just judgemental bullcrap.
OP's gpa shows that they are academically competent. There are a ton of things in their app which can be used to evaluate them, and which adcoms are used to sorting through. But the fact that they chose to skip a graded chapel attendance? That is something which a multitude of factors may have led to, and which frankly is only relevant to future medical school performance/behavior as a physician in a very limited set of circumstances, and even then it's the slightest bit of tangential relevance. So it bugs me to see such widespread, vehement judgement.
It's 7 Fs, that's why it's an automatic redflag. If I'm looking at an overview of OP's undergrad grades there are 7 Fs back to back to back to back to back to back to back.
Mr./Ms. Ad-com: "So OP, your GPA looks great. MCAT, EC's, LoRs are all solid. What's up with these 7 F's?"
OP: "Well Mr./Ms. Ad-com, I didn't go to chapel because it made me uncomfortable."
Mr./Ms. Ad-com: "So what did you do to address this situation?"
OP: "Well Mr./Ms. Ad-com, I just failed the class."
Mr./Ms. Ad-com: "So you had this revelation after becoming more familiar with this particular religion and, instead of transferring or going to a different school, you just failed?"
OP: "Oh no, my high school was pretty much the same flavor of Christianity. I really didn't want to go to this school to begin with. I didn't transfer or go elsewhere because of money and also my parents wouldn't let me."
Mr./Ms. Ad-com: "Okay... Did you attempt to explain the situation or find a work around?
"
OP: "No... Well, I didn't protest or ask for special treatment."
Mr./Ms. Ad-com: "So you did nothing. You failed a class every semester for 2.5-3.5 years..."