Should I tell my situation or request a possibly negative recommendation letter? I'm preparing to apply to PhD programs. My current master thesis PI used tactics to postpone the graduation of the students in order to keep them longer. I quarreled with him one time in order to get the degree. I sincerely apologized in front of lab members and him. 

He was the only faculty member who is familiar with my research. There is no supervisory committee. So I am concerned about the LOR from him.

Which solution might be better? Or is there other better solutions?


Do not request current PI for LOR. Rather, describe the fact he likes postponing his students’ graduation in the PS and the interview. This seems a bad solution. 
Do not request current PI for LOR. Say nothing in the PS or in the interview. However, if I am asked during the interview, should I say that he wants me to stay longer ?
Request current PI for LOR, which may be a possibly negative letter. However, no one knows the result. It is impolite to ask if he would write a strong recommendation letter for me. He has not denied my request of LOR directly, but he said he is too busy. I am not sure if he would finally write it for me.
"Too busy" means "I won't write a letter you'd like."

"Describing conflicts" with your supervisor will raise flags you do not want to raise.

Your choice 2 is the correct one.  If you are asked why you don't have a letter from a current faculty member, say your working relationship with your thesis supervisor was "difficult."  Do not say anything more except to answer further questions as briefly and politely as possible.  Let your transcript speak for itself.