I don't really understand how all this stuff works at the kernel level, but if you have a 64-bit kernel what would prevent you from also having 64-bit user programs?
There is quite a lot of surface area between a program and the kernel - C library, dynamic linker, system call interface, memory layout, droves of permission and sanity checking logic etc. that would need to be updated too. A 64 bit kernel is a first step
