You raise an interesting point, DC. I can see why they didn't allow the passage you quoted into the final cut of the film--it would have interfered with the masterful portrayal of Michael's evolution.
But, since I hadn't read that early draft until you posted it, I always attributed Michael's uneasy look at the funeral to two factors: not knowing who the traitor would be (note how he he keeps glancing around him, trying to see if he can spot the guilty party, until Tessio reveals himself); and, perhaps his realization that, with Vito dead, he's totally committed to the Mafia life, with no turning back. Yes, he really was committed before Vito died, but his father's demise cemented his fate.