Inappropriate relationships at my sons Catholic school

My son attends Catholic school. This is not a choice o made. He lives with his dad. This Catholic school is a really great school and has connections with several great colleges. Most of them are religious based but it our son has a chance to get a full ride scholarship to a college, religious or not we want to take that chance... My is with me for the summer, and my ex called me so upset because he found love notes in my sons backpack between him and somebody named Liam. My ex husband told me to go through his phone to see if I could find anything and I found out who this Liam person is... He goes to the Catholic school too. Based on these texts they have been in a relationship over a year and are even having sex. People find out... Things are going to shit... I told my ex that maybe this is a sign we should take him out of that Catholic school. Especially if they will ruin his life if they find out but my ex said our son isn't giving up this opportunity for a faggot boy and he better get it together. He told to talk to our son or he will...

They're both 17. The relationship isn't inappropriate.... But the school will think so...

Edit: You don't understand this school. They are strictly against homosexuality. Administration finds out the entire school will pretty much shun him. It will bet around, parents will try to get him kicked out. He will have help from them in getting into college. This has happened at this school several times before. I was never really ok with him going to this school or to begin with, but administration finds out, then... They will make his and this boys life hell.

Edit2: I want my son to live with me but I did 3 years in prison on drug charges. Its how I lost custody. My ex has the court in his favor