Something I don't think many people realize when it comes to the PL and their "brand" - the PL was created as a breakaway league, instigated by the then-elite clubs, to hoard more money and titles for themselves. They simply aren't going to tolerate an interloper like City coming in and destroying them all. That's why these "rules" were put in place to start. I mean, rules that allow some clubs to legally spend more than others? Are you serious?
So, while I'm sure the PL would prefer not to have these charges casting a shadow, it's not their biggest priority. Their biggest priority is ensuring City can't continue to dominate. That is everything to them. So they had nothing to lose pursuing these charges come what may.