That would have been a pretty serious betrayal of the crew, and especially of James. No one but her needed to know Fred had that sample or to ever learn he got it from her.
Giving it to Fred, however, was something she did only in the last extreme, and she immediately came clean about it when she didn't die. It was definitely a big breach of her crew mates' trust to have hidden the fact she didn't destroy the protomolecule sample as agreed, at worst it's a betrayal of the trust between Jim and her, but at the time that trust was wearing thin and Naomi wasn't so sure anymore that Jim wasn't turning into another violent "man with a cause". The word is too strong, and she has no allegiance to the UN or MCR. She couldn't consult the other three on that decision, not in the circumstances she made it in.
In her eyes, she was righting the balance of power and giving her son a chance at a better life growing up as a Belter. She made the final decision as she was convinced she would die, convinced too that the UN and Mars already both had the protomolecule (it was wrong). Naomi took her time to learn to trust Fred and Drummer. The decision to entrust it to Fred was not made lightly. Holden's increasing irrationality with everything regarding the protomolecule also made it pretty much impossible for Naomi to "come clean" early. The decision to destroy it was precipitated and fuelled by Holden's growing obsession. She was right to not want to destroy the sample immediately.