There is never a permanent solution. At any time, updates can (and in this case did) break people's systems.
More investigation is needed to determine the scope of this problem. If it is a general bug in the Linux kernel (or Ubuntu flavor thereof), which affects more people than just ImageJ users, I expect it will be fixed relatively quickly upstream. But if it is a bizarre interaction with the ImageJ launcher specifically, maybe not.
We are planning to migrate to a different JavaFX-based launcher eventually (see imagej/imagej-launcher#33 for technical details). You can generate an alpha build of this new launcher as follows:
git clone git://github.com/imagej/imagej
And there should be a platform-specific application bundle in there, including native launcher. You can also look in
target/jfx/native-nojre for a version of the app without an embedded Java runtime.
Note that I did not test this on Linux recently. I am not sure, but it may ask you to install additional utilities in order to successfully generate things.
Also note that while this process generates a standalone version of ImageJ2, the app may still have quirks. I am telling you this now mainly so you can test whether it works successfully, or also core dumps.