This is a tough situation and it will be resolved agreeably but all parties involved.
This post DOES NOT apply to this specific situation, but is a general statement. The specific details, parties in question, etc are private and will remain so.
My only input is career guidance is a two way street. If I put your name on your application and you get a job, my name remains in your shadow the rest of your career.
So your sins are my sins and the converse is true as well.
If you want a recommendation by me for my company, I will do my best to make sure you achieve your career goals because my name is my "brand". If don't share that feeling, do not ask me for a recommendation because it comes with a lot of responsibility and I will be on your shizzle if you're not respecting that. If it's just for a job and you plan on telling the world that "Welp, got mine, pull up the rope", again, don't ask. I don't care if you have nine starving children, need a job here and the sun will black out… my name on your recommendation means that you're part of "The Cause". Period. Don't care how busy you are collecting ex-wives, children and beat-up suitcases.
Want my name on your LOR or application? Oh, that's when the hard work begins because I have very high expectations. Continuous,
career-long expectations. The casual reader may think it's arrogant, cool, I'm glad you think that because if you do, you probably aren't a person who I would recommend anyway. Hell, I have a friend that will ask, "Do you have any internal letters of recommendation?" "Cool, so how do you know (whomever) and how did you meet?"

(read: Did you simply ride someone's jumpseat, got a card and they wrote you a letter like they've known you for years?)
Again, this post DOES NOT apply to this specific situation, but is a general statement. The specific details are private and will remain so.