Callie IS running away for Jude (at least in her head). She wants Stef & Lena to adopt him without her fucks up (kissing Brandon) ruining it. She is running away to avoid the situation, which ofc isn't the healthiest or the smartest but she is a teen. And yes, she is definitely needed for the show, she is a huge part of it and many of her storylines are great, don't give up on her yet!
I personally NEVER liked Brandon & Callie together, was never for it, and never got anyone who supported them... they really weren't it. And I will stand with you on the Callie-Brandon hate train, always!