Lapis wasn't portayed as in the right for fusion raping Jasper, and she didn't do it out of self defense. Jasper was already defeated at the end of Jailbreak and when Jasper asked Lapis to fuse to help her beat the CGs Lapis agreed because she was still pissed about being trapped in the mirror and wanted to take advantage of the opportunity to use Jasper as a scapegoat to take all her anger out on and keep her own prisoner captive. She admitted what she did was wrong, she just wasn't reprimanded for it because she got turned into a special snowflake wooby and characters rarely ever face consequences for their actions in this show no matter how god awful, unless they're Jasper or Lars.
Malachite was meant to be a portrayal of a toxic relationship that was unhealthy for both parties, the biggest problem with the arc was that Jasper did not get the help or chances to heal afterwards that Lapis did even though she was the one being trapped and used as a punching bag in the fusion and instead was left to fall into a downward spiral that ended with her feeling worthless and destroying herself before ever learning how much she had been lied to and how misguided her quest for payback against Rose was, though Rebecca has went on record to say that Lapis did treat Jasper unfairly and that Jasper is meant to be a tragic and self destructive character.
Malachite can be readdressed and the problem can be mended when Rebecca gives Jasper the healing, closure, and happiness she deserves in season 6. Her Malachite colored corruption scars and the depictions of Jasper/Lapis/Malachite outside of the show point towards there being more to come.