Its a very difficult situation. However the issue is if Apple takes a view, they open themselves up to legal risk - they are not the court so its not their place to determine copyright infrigement. Rather, if you get a court order stating infringement, then Apple has to take down the offending app.
Whilst yours may be a clear cut case, it is not too difficult to think of examples where it is not copyright infringement or is very difficult to prove - is Signal an infrigement of Whatsapp?
I don't think Apple could have done anything differently, to some extent it is your word vs. theirs and the right medium to settle the dispute is the legal system, not Apple.