This might sound counterintuitive, but I think the way to fix the whole tree/patch problem is to make killing trees EASIER and not more difficult.
First, get rid of the poison because it has really ugly connotations and it offends sensibilities. Instead of poisoning why not have a fourth option when clicking on trees. It currently stands as "harvest, pet, water" why not make it "harvest, pet, water, lumber". Lumber has none of the bad connotations of poison and it would allow to "normalize" the action of killing trees.
Lumbering should be as energy and time consuming as grinding is without the proper skill. That way it is annoying enough that the players won't want to do it too much.
In any case, killing trees is not so bad, you get more patches, people ALWAYS replant, actually, I think they love finding a free patch. What they hate is the depiction of a dead tree.
So to sum my suggestion up real nice:
a) get rid of poison
b) get rid of wood trees
c) get rid of the image of the dead tree
d) add lumber option
e) lumber should be energy and time consuming
f) make seeds cheaper for people who want to replant.