Reverse engineering isn't inherently good or bad, it's just a tool. That tool can be used for both good and bad.
I always recommend certificate pinning in order to prevent MITM attacks. I also recommend it if you're backend API gives out a lot of information about your product's "secret ingredient".
That said - certificate pinning can often be bypassed: http://blog.dewhurstsecurity.com/2015/11/10/mobile-security-...