Really? It was specifically written in the book. When the ministry fell the unforgivable curses were made forgivable (and indeed, Hogwarts changed from having 'Defence Against the Dark Arts' to just 'Dark Arts' and first years were tortured as were those who had detention with the Carrows. This is also why Snape sent 'Dumbledore's Army' members to have detention with Hagrid instead of with the Carrows!). Once the second war was over, under Shacklebolt there were major changes to rid the ministry of corruption (like say, allowing Riddle to rebuild his army while the ministry conveniently denied his return). Also, just like some others suggested, Aurors were allowed to use them in the first war. Not only that, with the exception of a certain spell that regurgitates it out (first seen [if you read] in The Goblet of Fire, when they found Winky with Harry's Wand, after Morsmordre [dark mark] spell had been cast by Barty Crouch Jr. with Harry's wand), no one would have known the spell was cast for 100% sure (remember in the second year how Dobby used a hovering charm yet the ministry refused to believe it was anything but Harry and ignored the fact they could have checked?). Oh, and Harry's wand was broken when he cast Crucio on Carrow so he wasn't even using his own wand (yet another thing neglected in the film).
Never mind the other obvious reasons, of course... like say, that there was once again peace and the death eaters that still lived (like the Carrows, who were in fact tied up in Ravenclaw's tower*) as well as those who collaborated with them (e.g., the toad-like Umbridge) were now imprisoned. Or perhaps that by Voldemort following through with the prophecy there were two choices that either of them could make:
1) Do nothing and ultimately be killed by the other.
2) Do whatever it took to win or in other words have the other die.
And the most obvious reason (as if this is really needed):
If it were not for Harry fulfilling the prophecy (that he was unfortunate enough to be forced in to) they'd all have been killed. The only reason the first wizarding war ended is because of Lily's sacrificial protection made Voldemort's Avada Kedavra backfire when he attempted to use it on Harry. This is mentioned by Voldemort himself in The Goblet of Fire, after he was reborn. Don't you remember him talking about 'old magic'?
This and more is all referred to in the entire series (at least for those who know how to read - they never interrogated Winky about Morsmordre in the film, for example).
*You could also ask the same question about McGonagall who used Imperio. Didn't know that? Oh, right, because that entire scene (same where Harry used Crucio on Carrow) was not in the film.
Also, I seem to remember that no, Lucius did not use or try to use Avada Kedavra. (I remember reading something about the actor specifically mentioned that there was no mention for what spell - in the script - to use and this was just the first one that came to his mind. I cannot remember too well as I read the book so long ago but I don't remember him ever even starting the incantation there before Dobby interrupted him).
Edit: Harry didn't only use Imperio on a goblin, either. He also used it on Travers, the death eater. A human. But again, they were made legal at this time. I still am dumbfounded that this is not understood. Think about it: do you really believe the death eaters who then had control over the ministry, would not allow it? They were the main users of them and they didn't care if someone was manipulated, hurt or killed and they didn't care how it was done either. In fact, they liked it (remember how Bellatrix told Harry you have to really want to cause pain in order to truly succeed in unforgivable curses? She followed with giving him a lesson by using Crucio on him. That's why he failed at that point and she showed him what she meant. Indeed, Harry even remarks about understanding it now, when he used it on Carrow in the Deathly Hallows!).