Coachella cares about making $. That's all there is to it. If they feel they can make more $ by having two festivals they will.
I remember when the new Yankee Stadium was announced. The "real fans" felt like we were losing tradition and history. Management didn't care, they knew they could make more money. So the fans had to accept it, the new stadium was happening. After the initial shock, we realized the Yankees did a great job with the new stadium. So good that people don't miss the old stadium anymore. They also won the World Series the first year in it, which helps. Maybe if GV gets Radiohead and Daft Punk (the musical equivalent of winning the WS) we will stop complaining.
I also remember when George Lucas first decided to make 3 prequels to Star Wars. The "real fans" were against it because Star Wars was perfect and they didn't want "more". Lucas didn't care, he knew he could make billions. The films were horrible but still made money. Now he made an animated movie and show, is making a live action show, and is considering making episodes 7, 8 and 9. So in this case, Star Wars became tainted and will only become more tainted in the future. If making artists play for two weekends forces GV to get Lolla '10 type of headliners (the musical equivalent of sitting through Star Wars Ep 1), it could be the end of what makes this festival special.
Here's hoping it turns out more like Yankee Stadium and less like Star Wars 1.