It may not even have been as clear cut as "no Spartans means the Covenant would've killed everyone". Perhaps ONI and the UNSC would've attempted a different project focusing on space defense instead of supersoldiers, like building the Super MAC platforms thirty years early. The Spartans had a high killcount, but the first chapter of The Fall of Reach shows full well their range of use; i.e. incredible on ground battles, useless against orbital bombardment. And without the Great Schism and the Arbiter's help, the Chief wouldn't have stopped the war.

But even then it's still not clear cut. Maybe having Super MACs above the colonies also would've led to inethical use; it is, after all, a giant gun pointed at a planet, and that has even more ramifications that thirty-plus soldiers. All in all, we can't fully know what would've happened and thus can't say the ethical or inethical course always would've been the right one.