You've said this "rebuild" a couple of times now. Curious as to why? I don't think their farm system is much to speak of anymore, but they have a good MLB core and a pretty strong pitching staff. A couple of good years of drafting and development, and they'll be fine. Maybe not great, but certainly not in dire straits. Signing Choo for a few years would help a lot.
Right now, the Reds are the third best team in the NL Central. I think St. Louis and Pittsburgh are likely to be better next year than they were this year. I think the Reds are more likely to be worse.
If they resign Choo, they're going to have to commit enough money that they won't be able to sign anyone else unless they massively expand payroll. Choo won't replicate this season even if they resign him and I don't think Phillips has much left in the tank. If those two slip it hurts the Reds pretty bad. And it's not certain they can even resign Choo.
I think Baker was simply a reflection of the team. They're good, but they aren't quite good enough. So you might as well go all the way and rebuild.
They have guys like Frazier and Cozart who are really pretty solid MLB-ers, just not good enough to put the Reds over the top. They could get some really nice prospects for those two. Bruce would fetch a lot as well. You could also trade Bailey as he has a lot of miles on that arm now, and Latos because he's close to free agency.
They don't have to make all those trades, but the point is they have a lot of decent assets. If they rebuild now, they may only have to punt next season. If they wait, they could end up in a Cubs-like 4-5 year rebuild.