The issue with Java is not a free software issue. It is a patent issue. Google (which uses its own implementation of Java in Android) and Oracle (which bought Sun Microsystem) are fighting on it: https://en.wikipedia.org/wiki/Oracle_America,_Inc._v._Google,_Inc.
It is perfectly possible to program in Java using only free software. Sun
Microsystem released all basic tools and libraries under the GNU GPL in 2006.
Since then, OpenJDK has been the official Java reference implementation. It
is in Trisquel's repository: the "default-jdk" package.
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