Easy - somewhat special - solution: Dont't exec "apt-get install ..." but "apt-get -y install ...". This will suppress any questions for confirmation.
More general approach: Runtime.exec() creates a process instance. What you are doing in your code is createing two proceses "apt-get" and "y". What you need to do is: Create one process instance and input the character "y" into the input channel of this process. This is achieved by creating the process (as you already do), gather a reference to its input and send "y\n" to this input.
The input is aquired by calling Process.getOutput() which gives you an OutputStream thats connected to the input of the process.
This all results in something like:
ls = Runtime.getRuntime().exec(
new String[] { "gksudo", "apt-get", "install", "PACKAGE" });
ls.getOutput().write("y\n".getBytes());