The Justice League is THE premiere DC superhero-team. And Wonder Woman being one of their premiere characters, naturally she belongs there.
That said, I wouldn't mind her being on the JSA under the following circumstances-
1. If its on Earth 2 or some other parallel earth/alternate timeline, then it totally makes sense for the Diana of that reality to be on the JSA.
2. If Diana is retconned into being an immortal who's been around for decades, if not centuries, and was once a member of the JSA during WW2. But given that they've just done Diana's origins again and established her as debuting after Superman and Batman, I don't see this happening.
3. Hippolyta as Wonder Woman time-travelling to the 1940's and serving in the JSA, which was how it was Pre-Flashpoint.