Since we have no proof that the clones would not be allowed to retire after hostilities, and to all the men who are killed in action, no, there isn't a lot of difference. What does it matter to some draftee, dying on the beaches or in the hedgerows of Normandy, that if he had survived this huge effort to make the world safe for communism, he would have been released to attend his own affairs, and resume the activities he was forcibly compelled to set aside, under penalty of punishment? "I would have given it back when I was done with it, if people to whom I exposed it, had not destroyed it" is not remotely an acceptable defense of theft, so why do so many people think it is an argument applicable to human lives?
The only difference is between how nice they are in doing a wrong thing. There is nothing fair about compelling people to fight and risk their lives. It is absolutely, unquestionably immoral as well as unconstitutional.
Just because the Kaminoans are better at it does not make them any more immoral.
And it's the same thing with the draft! That's even happening in some countries, that use the same conscription principle to make people work at other tasks that have nothing to do with your absurd common defense excuse. They keep floating the idea in the US too.

They didn't do the best and most ideal thing, but they did the best they could given the circumstances. No one actually thought through the morality or the implications for the long term. They saw what they were facing, they saw a solution, and rather than tear down the whole thing in mid-crisis, rather than trying to rebuild the boat in the middle of a storm, they acted to mitigate a wrong that had been perpetuated. Since the Republic was already going to force these men to fight, the best thing the Jedi could think to do was to take part, ameliorate the danger, help bring the war to a speedy and successful end (throughout RotS we see the Jedi pressing for strategies and operations to cut off the serpent's head, as it were, that they are trying to bring an end to the conflict as soon as possible). The only alternative the Jedi had, once the bills passed authorizing the military and emergency dictatorial powers, was a coup against the democratically elected government and in violation of the constitution, which was probably worse, since it is sucking them even further into their original mistake, of attaching themselves to the Republic.