I can successfully initiate a phone call within my app using the following:
[[UIApplication sharedApplication] openURL:[NSURL URLWithString:@"tel://123456789"]];
As far as I'm aware, because control is passed to the phone.app to make the call, once the call has ended, as far as iOS is concerned phone.app is the current app so that stays in the foreground.
There doesn't seem to be anything you can do about this at the moment. It might be worth putting in a feature request to allow for a "modal phone call" similar to
MFMessageComposer that allows you to send emails/sms within your own app.