We use a modified kernel. You can use the commands
apt-mark hold raspberrypi-bootloader
apt-mark hold python-tornado
apt-mark hold raspberrypi-kernel
to prevent it being broken (also true for the Tornado webserver).
As a side note you should generally not do apt-get upgrade regularly on a non-desktop Linux system. 90%+ servers in the world do not do so to avoid precisely such issues. The same goes with any custom software. It's really only "safe" to do on a desktop with only standard packages, and even then it can sometimes break things. This is in fact the reason why Linux keeps older versions of packages in the repositories in the first place.
We plan to release packages, but all the above will still apply, functionally the differences will be
a) possibility to update UniPi software via apt
b) not needing to use the above commands manually (they will be instead done by the packages during installation)
You are of course welcome to compile the kernel yourself against any version which you wish, it's openly available in our repository.