Let's start with ODI's. South Africa lost the ODI series by 4-1 and have pathetic record in Sri Lanka. The lineup for most ODI was this:
Ingram/De kock, Amla, De Villiers, Duminy, Du Plessis, Miller, McClaren, Peterson, Morris, Morkel, Tsotsobe.
When Smith is fit, we can expect him to be back in his usual opening position and same can be said about Steyn. Even though I like what I see of Morris, I still think Tsotsobe will keep his position. So the line-up when Smith and Steyn comes back is pretty similar to what you have posted except the fact that Tsotsobe will keep his place instead of Morris. So even by looking at that line-up I don't think the result would have been any different.
I agree with the back-ups you have mentioned. I would love to see more of Marchant de lange rather than useless Rory Klienvielt. F Behardien is also a complete waste as I have not seen him perform at international level a single time.