WhatsApp lost hundreds of thousands of users out of 450 million. Yeah, I bet they're losing sleep every night over that 0.1%.
It's about Facebook's brand.
There are many things Facebook might want to do, but it can't, because people don't trust them, and their every movie is a potential cause for outrage.
No company wants to be left with the only alternative of buying their way into success, and as you see this doesn't work quite smooth, either.