In this particular case, that to encourage people as far as possible to use the in-app purchases system is more favourable to the users.
It seems much more likely than "deciding to be evil".
For that matter, using in-app purchase is only favorable to users who stay entirely within the Apple ecosystem. One serious objection Amazon et al had to in-app purchase is that it (by design for privacy reasons, IIRC) didn't allow them to connect the dots between an iTunes account and an Amazon account, so they wouldn't have been able to give you access to your iOS-purchased ebooks on non-Apple devices. For that matter, they wouldn't have been able to give you access to your ebooks on a Mac for the same reason, which is particularly hilarious because Apple doesn't provide iBooks for Mac either (IIRC, you can buy but not read on the desktop).
No.
"Our philosophy is simple—when Apple brings a new subscriber to the app, Apple earns a 30 percent share; when the publisher brings an existing or new subscriber to the app, the publisher keeps 100 percent and Apple earns nothing," -- Steve Jobs
When Steve thinks something is better for the users, he says so (e.g., not supporting flash). Steve said this is about money. I believe him.