It will always possible to screw up your system if you bypass your distro's package manager. This is not unique to JACK. Just build a new Debian package (or RPM or whatever your distro uses) if you need a newer jackd.
I have many times read the manuals how to build your own debian packages, but it just feels a bit too complicated. I just wish there was an oneliner for that job. Or some way to just autocreate the dependencies that you have to fill in, that's the phase where I have always given up.
Tommi
