There are far too many conspiracy theories to this, most of which are way off the mark. Fact is the knockout was pre-planned.
The three IPL teams sacrificed a spot in the semis and finals for the greater good of Indian cricket. While Daredevils have four players (Sehwag, Gambhir, Mishra, Nehra) in the one-day side, Royal Challengers have two (Praveen Kumar, Virat Kohli), only the Deccan Chargers have none.
The Champions League Finals are to played on 23rd October (8 pm) in Hyderabad, while the India-Australia one-day series begins 25th October in Vadodara (9 am), giving next to no time for any pre-match conditioning to IPL players.
Even though there's no Deccan Chargers’ player in the one-day squad, and the Finals will be played in their backyard, such is the bonhomie among the IPL players, that Rohit Sharma and RP Singh (dropped from the ODI team recently) refused to play in the absence of their archrivals Royal Challengers.
As for the Daredevils, they sacrificed a semi-final slot.