Here's my two cents.
I think during scrutineering, the Ferrari Power Unit was found being able to do something stated outside the rules by the Technical Directives issued around the US GP.
This would explain both the lack of power in the late races and the dilemma the FIA is in. After Austin, Ferrari didnt use it, and before, it wasn't clearly stated as forbidden.
If disqualified for the season or the races before the TD:s, Ferrari would be certain to take legal action against that disqualification, and I don't think the FIA was sure of winning that battle.