The quarterback was benched by the NFC West side ahead of their game against the Atlanta Falcons earlier this month, before it was announced that he would be placed on injured reserve in order to undergo shoulder surgery earlier this week.
When asked if Kaepernick's 49ers career was over by reporters ahead of today's game against the Seattle Seahawks, Baalke said: "I wouldn't say that at all. I think people are reading into that. For me, where we stand right now, I wouldn't read too much into that right now.
"Right now is not the time to get into the particulars. Right now, he's no different than any other player that's been placed on IR. When that surgery takes place, then the rehab process, getting him ready for the offseason program's the next step.
"It was an injury that our medical staff looked at, and treated, and he didn't seek any extra treatment. But it was ongoing. It wasn't something that was all of a sudden, it just required surgery. Once again, this is something that they felt, from a medical standpoint, needed to be taken care of and addressed through surgery, which, obviously, if he has surgery, he's not going to be able to play. So moving him to IR is the natural move."
Kaepernick recorded 1,615 passing yards, six touchdown passes and five interceptions in nine appearances for the 49ers this season.