JonDo can already be used over Tor when it is installed inside Whonix-Workstation ™ (user → Tor → JonDo), see JonDonym.
Installing it by default.... Unsure. Only one person asked about JonDo... We're not very positive that JonDo will be pre-installed on Whonix-Workstation ™ by default, although we're totally against it.
All software in Whonix ™ by default should be able to update itself (or at least inform that it is outdated so it can be updated with only one command, such as torbrowser). We don't know if their Debian repository works for Debian Wheezy, which Whonix ™ is based on. Can you test it please?
We also wouldn't know what happens if they replace their signing key.
As Whonix ™ developers we can't really support the JonDo software. We don't have time to build JonDo from source code and ship a new build of Whonix ™ each time JonDo gets updated.
They have their own instructions in on their homepage and those may change over time. If follow their instructions and pre-install it and they change the instructions, Whonix ™ users will still have the outdated versions. What should we do in that case? Post in important blog "now follow these command line instructions and get JonDo updated if you use it"?
So this almost always requires either to offload installing it to the user or some cooperation from the original software project.
Whonix ™ is also quite simple at the moment and we don't know how the project would be perceived if Tor Browser and JonDoFox were installed by default.
Building Whonix ™ from source code, custom builds are always possible. To make this happen, it needs someone deeply caring about JonDo and contributing to Whonix ™. Otherwise it is very unlikely.