PixInsight works nicely on Ubuntu 16.04, so it is definitely able to run on it. It's just a matter of installing a couple of required packages, as you have discovered.
Is it a big issue to use the new libgstreamer release?
Yes, because Pixinsight must run on older Linux distributions. Our reference distribution is Red Hat Enterprise Linux 7.1.
On the other hand, including gstreamer in the standard PixInsight distribution archive is problematic, since this library has many and complex dependencies. I'll try to include it in the next version, though.