Is my process waiting for input?

If the console application has some sort of prompt waiting for input, you could periodically parse out the console output text using the Process.StandardOutput property of the process and wait for said prompt. Once the proper string is detected, you know that it's waiting for input. See http://msdn.microsoft.com/en-us/library/system.diagnostics.process.standardoutput.aspx.

Depending on what the 3rd party process is doing exactly you could try polling its threads' states:

foreach(ProcessThread thread in process.Threads)
    if (thread.ThreadState == ThreadState.Wait
        && thread.WaitReason == ThreadWaitReason.UserRequest)
            process.Kill();

Failing that... you can try to

process.StandardInput.Close();

after calling Start(), I conjecture that an exception will be raised in the child process if it's trying to read from standard input.