First, Apple isn't removing Java from OS X. They will stop shipping their customized version of Java in several years.
Second, every popular piece of software has vulnerabilities. So if this warrants the removal of Java, you should remove Safari and the BSD kernel from OS X as well.
There is no BSD kernel in OS X. The entire OS is Darwin running an XNU kernel that has a BSD layer within it. There is no way to remove the BSD layer without removing the entire OS.
Second, every popular piece of software has vulnerabilities. So if this warrants the removal of Java, you should remove Safari and the BSD kernel from OS X as well.