That's why if there's gonna be another story with Rust, it has to be before the events of Season 1, or possibly during that "missing" time period. But filling in what happened during the gap would almost have to tie in to the events of Season 1, otherwise there wouldn't be much point. Or maybe Pizzolatto can come up with a relatively self-contained story, some series of events that happened during that time which is compelling enough to warrant its own season. It would be cool to explore that, and the character, but then it would almost seem wrong to not have Marty there as well. Rust was awesome, but the interplay between the two of them was part of what made the show.
In fact, part of the whole setup of the True Detective series is the two leads. If Rust's new story doesn't have Marty in it, then Pizzolatto would need to come up with another character, equally awesome or at least close enough to share time with Rust Cohle.