It's pretty tough for betfair to LOSE money. As mentioned in the article, they are a peer-to-peer bookmaker. They match you up with someone willing to take the opposite bet, and you either win or lose against them, not betfair. Betfair are essentially an agent, who take a slice of the winnings, for matching you up with someone willing to gamble with you. The other side of this is that by arranging these bets, betfair are the people holding on the money before giving it to the winner. Although they won't take the slice they would have if they just paid out, I'm sure £3m in their accounts will accrue a little bit of interest before this is settled. They certainly haven't thrown out any cash whatsoever.
The irregular betting was that after Davydenko won his first set, a lot of money was placed on the other guy (Arguello), which is not what you'd expect. Davydenko's odds actually lengthened after winning his first set, because around £3m was staked on Arguello, both just before the match, and during the first set. This is around 10 times more than you would expect to see staked on a match like this. If it was Nadal v Federer, at a major tournament, then maybe, but not this. After all the money piled on, the apparent favourite to win (although still 2nd favourite with betfair) got an injury and retired.
The real implication from this is not that someone has tried to defraud a bookie, this happens all the time, with little sympathy. The real story is that for this to have happened, Davydenko must be in on it. How else would you know he'd definitely pull out, especially after winning the first set? The ATP will pursue this a lot heavier than betfair will.