Maybe I've completely missed it, but I don't necessarily believe Link has to "fail" for timeline A to happen. I'm actually kinda surprised that nobody's thought of this before now. In Oot, when Link pulleth the master sword time doesn't just stop. The timeline continues without a Link and with Gonondorf getting inside the sacred realm. Oot Adult timeline then happens and everybody knows that song and dance "Ganon sealed, link sent back, flood ect.ect.ect." When Zelda sends Link back to the past she sends him back to before a) young Link and Zelda ever met b) or just right after their meeting. At either point Zelda hasn't fled yet showing that Ganondorf hasn't made his move yet, and he also has no access to the spirit realm. This accounts for timeline B, however there still is the timeline where Link disappeared and Ganondorf had access to the spirit realm. This timeline would have no Link returning seven years later so the people have to find another way to beat Ganon. This is how it makes sense to me.
However, despite the fact that I just defended it, I'm not entirely happy with this timeline. I'm upset that there seemed to be a good build for a OoT-TP-LttP in-game that appears to have been completely thrown away. FSA to me seems tacked on to TP for no reason. And there's no good explanation on the time difference between LA and LoZ, where did the master sword go between games (there's no LttP for it to "sleep forever"), and how did the Triforce go from being complete in LttP/OoS-OoA "i.e. Ganon loses his" to Ganon getting it back and the Triforce of Courage being put in a temple (which would suggest that the Triforce was broken up well before Ganon's return). For all this to truly work for me Miyamoto and/or Aonuma (probably both) will have to come out and explain their thought process.