The real problem for most users has been the lack of support for understanding the ZFS structure. A bunch of programs see ZFS's free space as beeing in KB instead of GB or TB. So you may have 20TB free, but it thinks you might have 20KB free. So it errors out with something equivalent to insufficient disk space. Unfortunately, since every single program handles its calculation of free space differently, and each also handles a full drive differently, unless you are a linux pro you aren't likely to have much success in fixing it. We've had people with years of linux experience give up because too many programs are just too broken to deal with the problem.
Then you have to consider potential updates to the programs.
Then you have to factor in potential changes to ZFS and FreeNAS as time goes on.
The whole idea if Linux in a jail, while it sounds great in theory, doesn't seem to be too "ideal" in practice. We've gotten lots of complaints, but it's not something that really falls within the realm of things that the FreeNAS team should or can fix.
If you are really wanting/needing Linux, you can do Virtualbox in a jail. I wrote a step-by-step guide for setting up and installing Virtualbox, but it does have hardware needs.. plenty of RAM, fast enough pool, and virtualization extensions must be supported on your CPU for 64-bit VMs.