One of the largest fears of the people judging your applications is that they will be falsely accused for some "serious misconduct". And now you want to apply to them, accusing your ex-prof with a "serious misconduct" in your application.
You are harming yourself and not him.
If you decided to not start anything against him, you abstained your right to intervene. Accusing a prof with some serious is a really hard thing, best if you are far, far away from anything even similar to that.
If you didn't do anything at the time he committed the misconduct, and if you "defame" him later, retroactively, it looks very bad for you.
Even if you have documents and proof. The first question what would you hear: "And why didn't you do anything at the time?"
Despite that you had the obvious reason to not do anything at the time.
Furthermore, the people judging your applications probably won't know what he did. The strength of your application should be the possible strongest in their eyes, and not in yours. Missing his recommendation letter may be understable - for you -, but it will look very differently for them.
They will simply think that you don't have a recommendation letter because you are bad. And anything what you say about the case, will most likely further decrease your estimated value in their eyes.
Logic would dictate, the best would be in your case if you could somehow utilize the power of your proofs to let him to help you on your academic career. However, any possibility I can think for that, would be far more risky for you, as for him.
I am sorry to say, but I suggest to play this: "everything were happy, look what a wonderful LoR I've got". This maximizes your chances in the future.