Here's a patch that should clean up these runtime dependencies. 
It's a bit specific to this particular case, but I think that 
might be fine for now.

I think it would make more sense for native inputs to not have 
their paths included in LIBRARY_PATH. Does it even make sense for 
them to be there? I thought LIBRARY_PATH was for compilers to find 
dependencies when compiling so they can link their output binaries 
against them. Having native inputs show up there seems wrong.

I'm in the process of rebuilding Java from icedtea-8 upwards to 
check, but I have already tested that modifying openjdk 9 and 10 
leads to "guix gc --references" show that openjdk 10 does not 
depend on openjdk 9. I have also tested that I can run some 
complex Java programs on my machine using the openjdk 10 built 
using this patch.

Carlo