I wonder if that wasn't intentional from the writers' point of view? In "New Ground", everyone had to trust Daniel to do the right thing, say the right thing to save the entire team. Then you have 'Maternal Instinct' where Daniel is once again the rallying point for the trust thing. That might be worthy of a meta on the issue of trust in these three episodes!
The team trust wasn't irrevocably broken, but had to be quite fragile at the beginning of the mission. The remark that Daniel made about not trusting Jack's command always seemed a bit off to me until I read a fic where the author had Daniel saying that although he questioned most of the military decisions Jack made, he trusted JACK himself. Kind of one of those fine lines, but it helped me to see where Daniel was coming from.
As for going back and changing, I think you should leave it as you see it. I don't advocate changing something you've written just because someone else sees it a bit differently. Just a different way of looking at the same situation.
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The team trust wasn't irrevocably broken, but had to be quite fragile at the beginning of the mission. The remark that Daniel made about not trusting Jack's command always seemed a bit off to me until I read a fic where the author had Daniel saying that although he questioned most of the military decisions Jack made, he trusted JACK himself. Kind of one of those fine lines, but it helped me to see where Daniel was coming from.
As for going back and changing, I think you should leave it as you see it. I don't advocate changing something you've written just because someone else sees it a bit differently. Just a different way of looking at the same situation.