I like HH because neither one of the choices sits perfectly well with me: fleeing Zion may just end up putting off them losing innocence which will probably eventually happen, fighting the White Legs destroys what innocence they had.
I think I was one of the few who ended up siding with Daniel, partly because I think the value of their souls and innocence is greater than Zion. But also due to Clark's entries. He is a man who has lived with death and killing for years and it has brought him no peace. However, with the children I believe he is able to eventually find some peace.
He does tell them to strike back if attacked, but I think their innocence mattered more to him, from his final entry:
"I wish them well. It's been a gift to me, at the end of it all, to behold innocence."
In a world wracked by war and fighting, perhaps some innocence is needed to stop it ever happening again.