AITA or a religious nut job

I'm 18(F), live with my 18(F) roommates, let's call her Alyssa. We go to a Christian college in a state apart of the Bible Belt, where I grew up. Alyssa is a Christian but from the Midwest. We have similar basic beliefs but different practices, this is not the issue. I have a best friend with the same beliefs, Charlie (18F) who lives in our dorm hall. Alyssa and I are on the same team and committed earlier than Charlie or we would have roomed together. Charlie’s roommate dropped out, so she has a room to herself and a spare bed we use as our couch. 

Charlie and I both believe in no sex until marriage Alyssa does not. I do have a boyfriend (18M) who goes to school elsewhere. Alyssa and I both freely use the room for our own activities. Alyssa does so with her friend with benefits, I’ll call him Chris (18M). Chris will not commit to a relationship with Alyssa, but she really wants him to. Chris has a room to himself in another building. 

During our first semester, I left the room for them to have time together for an agreed-upon time, 1 hour. I returned 30 minutes later than agreed on so they could have enough time (it was late, and I had an 8 am). I made it extremely obvious I was back and yet still walked in on them. It was so awkward. This got turned around on me because I didn’t wait for an all-clear text. Which was understandable maybe I should have, but also, they knew I was coming back soon as I was in Charlie's room waiting for them to be done. 

Things were tense for a while because no one wanted to admit they were wrong. Alyssa and I have been attending FCAs and religious events together and focusing on our relationships with God. One of Alyssa's main things she wants to do is to stop having sex with Chris until he puts a label on their relationship (he won't). 

I have tried to remain out of that conversation with her because we have differing beliefs and it is not my place to judge anyone, as stated in the Bible. I will admit I did cross a line with this. There's a section in Philippines that talks about sex before marriage, and I brought it up to try to support her in her decision to not have sex with Chris until he puts a label on it. I did apologize for this; however, I didn't even realize it was wrong until she started talking about and confronting me about it at lunch in front of our friend group. I told her that I would rather talk about our issues in private where we could talk it out one on one. 

There was another instance where I got into a bad argument with my stepdad and had a full breakdown about it in our room. I had finally started to calm down and get my crap back together and they started making out in front of me. This was a common occurrence up until this point, but this was the final straw for me. A couple of days later we ended up having a nice chat where we talked everything through and all was well. 

Moving onto the second semester, she went back to saying she would not have sex with Chris until there was a label. Within about 3 days of being back, she had sex with him. A couple of days later we were hanging out in Charlie's room at 11 at night. Chris and a neighbor were in the room with the three of us. Chris and Alyssa were all over each other on the “couch. They get up and I'm told they're going to the room. Now this is about the time we both are normally wrapping up and going to bed. So, I’m like great I was exhausted and was not given an I'll text you when it’s good to come over and they left before I could say something. I accept my fate and end up falling asleep on the couch. This is a crappy dorm bed, and my back is killing me the next day. I had to walk back to our room to put a bra on and brush my teeth because I couldn't the night before. 

We had morning weights so had to be up early and ready to go. I slept like crap and was noticeably exhausted for weights. When people asked why I was so tired, she answered for me saying I went to bed late. 

Later while stretching my back, she asked me why I didn't come back that night. I said what do you mean, I wasn't given a Hey I'll give you a text or anything as we both normally do when taking up the room. She goes on to say well nothing happened, as she was elated, she was able to get through a sleepover without having sex with Chris. I said while obviously something happened and pointed at the visible hickey on her neck from the night before. I then said something about her already going back on the whole no sex thing so how I was supposed to know I could go back in the room especially after I had already walked in on them. She didn't respond and continued having a great day. 

I did not have a great day; I decided it was best to go home for the day and take some time apart. I came back in time for us to go to FCA. After FCA finishes we normally hang around and talk with friends. I didn't stay for the whole time because I was still exhausted. Something was said and I guess it came off in a way that was peeved and she only thought to ask me what was wrong then. I was taken aback because I thought I made it clear earlier when I was upset, I was locked out of my room for the night with no forewarning. I decided to leave it there because I didn't want to make a scene or start something in front of people. We've been walking on thin ice, and she has been telling people we're having problems again. I really wish she would say the same things she's saying to other people to my face so we can work things out. I don't know how to bring things up or talk it out and am trying to give her the benefit of the doubt because a family member is dying back in her home state.