You make some very sound pints points but, equally, I would suggest that it's practically certain City's being charged by the Premier League has been mentioned at governmental levels.
City believe the club is being mistreated. (Probably because they ARE being mistreated). They are a multi-billon pound company with the strongest of ties to Abu Dhabi. Of course, the AD government are going to, at the very least, express concern. It's inevitable that this concern will be couched in pointed language ("thought this was a place where we could do more business buuut...." etc).
I'd agree that it wouldn't go so far as outrage and explicit threats but the UK government, in spite of a great many acts and appearances to the contrary, aren't fucking idiots. (Well, not entirely).
I imagine the Premier League will have been warned that they'd better be bloody sure they can irrefutably defend any awards they make against City.
And rightly so. Any government would do the same to protect its citizens' foreign investments - and not just its highly-connected citizens either.