I love an Apple pile-on as much as the next guy, but this really isn't that controversial. Apple doesn't want you needlessly gathering info (including tracking info, which is personal info, so "just" a username and password would count). The only things you can put behind a user/pass wall are things that require account-based tracking. Apple's letter was pretty clear about this.
I don't know how much data this app needed to be input before operation. But I understand Apple's concern. Requiring a registration with lots of data before an app can be evaluated is annoying. Also the app can be easily be changed to get accepted.
This does indeed seem odd. I've never heard of any other cases were an app has gotten rejected because of this. At least, not in a case where it was publicized. Hopefully more info will arise on this issue.