They were. According to the Zero Collection timeline, X's soul kinda "shattered" when he sealed the Mother Elf, and a piece of which wound up in every Guardian...somehow... I'm not really sure how that works.
Anyway, I'm willing to bet that X, while respectful of the Guardians, did not believe that they would turn on his copy. Them being unfamiliar with the original makes this a bit more plausible; if one X tells them to kill another X, why listen to the ghost over the in-the-flesh guy?
There's also the fact that, based on the Z1 encounter, we can safely assume that Copy X outclasses them power-wise.
Zero was X's best hope. Not only is he the only one reliably strong enough to get the job done, but he also follows his beliefs without hesitation even when it means getting his hands dirty.
Same applies to Neo Arcadian policy after Copy X was destroyed, however on that note, Harpuia showed some promise in trying to keep the peace. The damage had already been done, policy discriminating against Reploids already in place, and the Resistance branded Mavericks, before Harpuia took command. Despite that, he was extremely nonaggressive in dealing with the Resistance, his only offensive against them being retaliation for Elpizo's Righteous Strike. He knew the Resistance's location throughout Z2 yet did nothing. Hell, he did worse than nothing, he returned Zero to them. He also left the Resistance go during Z3's intro. Harpuia did not wish to destroy any more Reploids, but his allegiance was still to humanity. Thus it is only when Weil and Copy X turn on humanity that Harpuia's faith in Neo Arcadia is shaken.