Tyrus was exactly what the Spurs needed in terms of skill set to compliment Tim and overall youth and athleticism. There's no doubt about that.
There also wasn't any doubt, at least in my mind, that the team that got him was going to get a player on his best behavior and playing at his highest level possible; Thomas is out of guaranteed money.
But acquiring Thomas wouldn't have made this team a champion and the questions about whether he'll mature or be the player he's capable of are legit. And if the Spurs didn't view him as a better prospect or fit than Splitter (fit as in Spurs material; Thomas would be a much better fit with Tim, imo), than it'd be hard to justify essentially taking a flier on a player for next year that could cost you someone you hold in higher regard.
There's no guarantee Splitter will be coming over, and there's no guarantee he'll be anything more than serviceable at the NBA level. But the Spurs believe he'll be here next year (from the mouths of both RC and Lindsey) and not pursuing Thomas makes sense in the aforementioned scenario.
They just better hope they're not left standing at the altar (and that the Thomas-Splitter comparison is viewed in a favorable light a few years from now).