I think this is one of the fundamental misunderstandings that's happening. Arsenal, Everton, Brighton etc haven't done anything wrong re shareholder loans as the current rules (that City voted for btw) state that shareholder loans don't bear interest.
City have subsequently challenged this (and had this challenge upheld) meaning that moving forward this rule is likely to be amended. At that points clubs will need to comply with it but that's only after an amendment is made. At the present moment it's perfectly legal - I suspect it won't be after the rules get amended (assuming 60% of PL clubs vote for it - they may also decide not to of course).