Going anywhere near a growing tree is a bad idea, because there's a chance it will permanently stunt its growth.
That said, I don't think taking items from it beforehand will harm it, in and of itself. The resources' quality are based on the growth progress, but it might be worth the risk to grab some.
If it seems to be taking way longer than usual to hit the next growth stage, it's probably stunted. I think all stages take the same amount of time, so yeah.
If they aren't just tiny seedlings, you can chop them down. If they are, I think you're stuck with them...there was a recent thread about them, but that seemed to be the conclusion.
if the base of the tree, the roots, seem to have grown bigger than the leafy part should warrant, its likely stunted. Most common causes are fences, houses, palisades and other trees
Learn from the mistakes of others. You won't live long enough to make all of them yourself.