Where did you read/pick up on all this back story? It sounds interesting.Of course he was doing the best job of protecting Sam's interest. If he wasn't, then he wouldn't even be on the board. And Sam did it because there were more people who took over Encom as far back as 1990 (can't remember exact date), where the board fired most of those who were on Flynn's side in order to take the company "in a new direction." Since Sam owned most of the stock for Encom, they couldn't fire Alan because his job was to make sure that Sam's interests were protected. And they figured that as long as Alan was still out of the way, those that took over the company could "continue to do whatever they want."
So, again, Alan was doing the best job protecting Sam's interest within the limitations he had. Not to mention, he
set up the Flynn Lives movement with RAM, which lead to the page from the Arcade getting through to Alan, Sam getting onto the Grid, finding Flynn and eventually exiting, and leading Sam to step up and take charge.