Even in the movies, the Jedi seem to be unhappy, or at least conflicted, about using the Clone Army. However, they have been wringing their hands and lamenting about their need for an army, so when one shows up unexpectedly, they realize that they have to use it regardless of any moral reservations they might have.
OBI-WAN (V.O.) ...I've never heard of a Jedi called Sido-Dyas, have you, Master?
MACE WINDU No. Whoever placed that order was not a Jedi, I can assure you.
OBI-WAN (V.O.) I have a strong feeling that this bounty hunter is the assassin we're looking for.
YODA Who he is working for... discover that, you must.
OBI-WAN (V.O.) I will, Master, and I will also find out more about this clone army... May The Force...
The hologram switches off, and OBI-WAN fades away.
WINDU A clone army! Ordered by someone in the Senate perhaps... Someone's out to start a war.
YODA Inform the chancellor of this, we must.
WINDU Who do you think this impostor Sido-Dyas, could be?
BAIL ORGANA The Commerce Guilds are preparing for war... there can be no doubt of that.
PALPATINE Count Dooku must have made a treaty with them.
MACE WINDU We must stop them soon before they're fully ready.
SENATOR ASK AAK The debate is over, we need that clone army now!
BAIL ORGANA Unfortunately, the debate is not over. The Senate will never be able to approve the use of that army before the separatists attack.
MACE WINDU The longer we wait, the stronger Dooku's armies become. We cannot wait for the Senate to make up its mind about granting the Chancellor emergency powers, in order to be able to use that clone army... We have the authority to go now. We must go now.
All of the JEDI COUNCIL nod their approval.
YODA Agreed, Master Windu. Two hundred Jedi send. Enough, let's hope they are.
OBI-WAN (continuing) I must admit without the clones, it would not have been a victory.
YODA Victory? Victory, you say?
OBI-WAN turns and looks at the sad little Jedi sitting in the Council Chamber. Apart from KI-ADI-MUNDI and PLO KOON, who is wounded, the Chamber is empty.
YODA (continuing) Not victory, a defeat, it was... Master Obi-Wan. Begun, the Clone War has!
- All quotes above taken from Star Wars: Episode II: Attack of the Clones
So the Jedi need an army, they find one, have reservations about using it, but time constraints and strategic considerations outweigh their concerns, and they deploy the clones. There isn't much time for them to debate the ethical dilemmas of using artificially obedient slaves to fight the war, but their uneasiness doesn't go away - it remains so pronounced that Yoda even calls their first victory a defeat.