I would argue that the end should never justify the means. If the French Revolutionaries genuinely wanted to build a society based on liberty, equality, and fraternity, then they should have used appropriate methods. It's difficult to see how such a society can ever be built upon the foundations of terror and bloodshed.
Although it's difficult if not impossible to justify The Terror, there are reasons why it came about when it did, and it's important to understand those reasons to gain a broader picture of events. The Terror came out of a period of great political turmoil and conflict. The crowned heads of Europe had waged war on revolutionary France, and there was a growing sense of patriotism among the French people who felt they needed to defend "their" revolution against the imminent threat of foreign invasion.
When people decide to take on a foreign enemy, they invariably also look for enemies within. (A good example of this in American history would be the McCarthy witch-hunts of...
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