I disagree with this assertion: "my feeling is that conflict of interest in journalism is between a journalist and his employer, not between a journalist and his readership."
A lot of people view Arrington as the face of TechCrunch and I feel like his stories drive a significant amount of traffic to the portal. I, for one, know that I read stories with his name on it -- even if I'm not terribly interested in them.
But, if Arrington's showing favoritism or is holding back, simply because he's invested in a company, it makes TechCrunch less relevant -- since someone else will break the story, or it may be biased. (And, let's be fair -- nobody expects complete impartiality from an investor. They're already partial, else they wouldn't be investing.)
To quote Arrington, "There’s a period of time with any investment when I know an investment is possible or likely but it can’t be announced yet. During that time I don’t write about the startup at all, because I can’t disclose the investment. When another writer wants to break a story we may have to hold that story, or it becomes a forcing function in announcing sooner." And this is the hart of the debate.
To address your other point: I know many, many, many journalists who have incredible integrity -- just avid news consumers today are becoming disenfranchised by news media (and I'd like to point out that Wikileaks, Twitter, and blogs are none of the above) does not mean that it does not exist. Would you really rather go to the biased news source if the unbiased one was right next to it?
This is the type of decision that is an inflection point -- because Arrington's refusal to stop will allow a lot of tech journalists to begin lobbying hand grenades at any unfavorable TC press ("I sure hope that Arrington doesn't have a hand in that! hahaha.")