Apple is requiring app updates to support 64-bit executables by June 1st. We've known and have been preparing to ship a 64-bit build of our first product for several months. The only way to create a 64-bit iOS build is to use Unity's new IL2CPP technology, which compiles C# code to C++:
The Future of Scripting in Unity
An Introduction to IL2CPP Internals
Unity 4.6.2 iOS 64-bit Support
The additional memory utilized by IL2CPP builds vs. the previous Mono-AOT approach is ~10MB for our code with an empty scene, and >30MB with everything running.
We've also tested the latest patch, Unity 4.6.5p4 (which is supposed to use less memory on iOS) with the same results.