The Queen already knows the pain of that sort of relationship however here she understands that it would be wrong of her to force her son into an unwanted marriage by separating him from the one he loves truly. She is prioritizing her son as much as she can as a Queen. She can't rescind an engagement that was made years in advance to a nation more powerful than theirs who can very well attack if offended. Also, she knows the prospective bride is no match and unworthy of the Prince so there is no way he would come to love her in future by any chance. Her proposition is her giving him a glimer of happiness in his distressed future bc Alphonso seems a straight up gentleman who would not want to tarnish his loved one's life and honor by making her a mistress instead of honoring her as his wife. He would probably blame himself for the rest of his life yet she would be the only solace he find away from his life as a King.
It's always happens to the polygamy society in the past. The queen must be full of power of comes from a decent family, while the mistress can be anyone so most of the time, a king married a queen whom he didn't love and kept his lover as his concubine
So the king marry the queen for power but mistress rubina is his actual lover? Is that why she proposed that idea to the prince? Because as a person with a great responsibly, the subject is the first thing he should put and his feelings is the second? This is so sad :'(