They lost a major battle.
Nothing can push a rapper out of the public eye faster than another rapper. Kool Moe Dee ended Busy Bee. LL, Kool Moe Dee and KRS-One MC Shan. For every instance where beef spurred the rappers to do better (Nas and Jay being the classic example) there are plenty of instances that ended less happily for one of the combatants. (Think Tip and Flip.)
When 50 went up against Ja Rule, Ja was one of the hip-hop's biggest stars. But 50's disses weren't generic; they honed in on what other people were already whispering, articulating the market's reservations. Ja was relying heavily on cheesy rap ballads for his success, blatantly emulating Tupac, and, yes, sounded like the Cookie Monster. These ideas, while hard to deny, hadn't hurt Ja up to that point. But once 50 said them out loud, in public, they stuck. When Ja tried to punch back with Blood in My Eye, an album almost entirely devoted to anti-50 battle rap, he'd already lost. Ja was out of his element, going away from his strengths. The album flopped. Ja's career has never been the same.