I personally believe Harbaugh felt Kaepernick wasn't the right guy, and Baalke disagreed.
You have to remember Baalke was the personal responsible in the final say of drafting Kap.. He is the boss under York and what he says goes and there has already been numerous reports about how Harbaugh did not like that Baalke had control over certain things that he wanted to have control over as a coach..
And now for the Fact that Baalkes daughter tweeted "The 49ers don't want you anymore Roman" blah blah... Then she deleted the tweet and then account following with the Baalkes apologizing for the tweet.. That right their shows Baalke himself didn't agree with the OC and it had nothing to do with the Quarterback..
Think about it. Harbaugh obviously is defending Roman saying hes the right OC for the job and maybe saying Kapernick and the O just wasn't performing the way they should have been (aka the rift in the locker room) and then you have Baalke saying no, the wrong plays are being called hence his daughter saying Roman the 49ers don't want you anymore, but Harbaugh never fired Roman, and then Baalke led to the "mutual of parting ways" with Harbaugh therefore getting rid of Roman.
[ Edited by SundayTicket on Jan 16, 2015 at 4:17 PM ]