Oh, yeah, I totally agree that this wasn't the reason (seeing as it wasn't in the game yet), but the two men quite obviously did not see eye to eye, and neutralizing Eamon made a lot of sense from Loghain's POV.

...it's one of the few things that I'm totally in his camp over. Like, the guy was a problem. Tough luck that he had to be neutralized for a while. I mean, better to risk killing him than to risk a war with him and destroy many.