I think the two original issues are...
1. Russell Brand & Jonathan ross making the phone call and their conversations in regards to it.
2. The pre-recorded episode being approved for transmission.
Interestingly according to Five Live the producer of Russell Brand's programme is an employee of Russell Brand, as it is indepindependent production by a company owned by Brand and his manager. Bearing this in mind it's fairly easy to understand how the programme got transmitted.
Up to the Daily Mail picking up on the incident there had been only 5 complaint (mentioned on Newsnight). Probably due to his wages Jonathan Ross is disliked by many in the media and with his involvement the media picked up on the headline and persued the story. I some TV media such as ITV (probably also Sky) were wanting Ross sacked, as it's been reported Michael Grade at ITV is keen to sign up Ross.
I think suspending Ross without pay instead of sacking him was the best option, baring in mind the pressure the BBC was under after the snowball of complaints. By him not earning about £1.5 million and being suspended for 12 weeks it shows they are taking action, however prevents rivals from hypocritically signing him up.
To err is human, but to really screw up you need a computer.