He didn't turn any 49ers offer down. He opted out because they were planning to cut him. Kyle Shanahan then brought in his own QB (Brian Hoyer) and drafted a QB (C.J. Beathard).
If Colin Kaepernick had not decided to opt out of his contract, the 49ers would have released the QB.
www.espn.com
The 49ers didn't give Kaepernick a choice to return. How do I know? John Lynch said it:
GM John Lynch confirmed as much this week
www.cbssports.com
"Brian Hoyer was one of the guys we pursued.
Once we pursued him, we didn't see Kap as a backup that would really fit in that scheme and we communicated that to him. So I think we've been very up front with it. But I think that is a fair characterization. Yes, he was not going to be here under the construct of his contract. We gave him the option: 'You can opt out, we can release you, whatever.' And he chose to opt out, but that was just a formality."