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We have fixed the issue in the latest version of InDesign, Id 15.0
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So it turns out, if you select the option "Fully Justify" for "Single Word Justification" all the issues, except for the special characters being broken apart from the lines they should be on work. So it is very close to being perfect! Just need those special characters to stay on the same line as the words they are part of.
But a special unexpected bonus - it looks like I can get spelling check to work!
@Abhinav Thanks so much for the update! It appears while justification is much better than before, some of the same issues still occur. First, line-breaks occur on special characters when they should not (parenthesis, colons etc. should not be allowed to break but should stay with the character they are next to). Also, in certain cases, words still go outside of the margins. And it appears hyphenation no longer works (it works in CS 5.5). If you need any files from me, don't hesitate to ask. I've attached some screen shots.