I think the OP makes some good points, but I would add that the declining ability and productivity of Ray, KG, House and Sheed are probably causing issues too. Lets compare PER from the championship season to this season:
R. Allen PER 16.60 vs 13.86
E. House PER 13.17 vs 12.39
T. Allen PER 10.81 vs 14.32
R. Wallace PER 17.13 vs 14.36
G. Davis PER 11.40 vs 11.08
K. Garnett PER 25.42 vs 19.77
R. Rondo PER 15.75 vs 19.93
In the championship season, Ray was clearly the best shooting guard, Sheed wasn't here / Baby was the backup four, and Rondo was just above average.
Looking at this year, Tony could make an argument that he should be starting. Davis thinks he is better than Wallace, and their PER's are close - plus he was the starting power forward of a second round playoff team last year. Finally, Rondo has replaced KG as the best player on this team - and over the last few games it is not even close.
When roles change and power shifts, conflict follows.