The arguments you raise (machines being "less dependent on nature" and that they could discover new power sources) don't in any way alter the answer given by the movie. They're basically accusations of it being a plot hole.
If you read the answers to the meta discussion on plot holes I just linked, you'll see that the discussion is primarily about answers. The consensus seems to be that "plot holes" as an answer is okay, provided the answer sufficiently explores in-universe answers first and foremost (i.e. they either show effort to find suitable in-universe answers that don't seem to be present, or present in-universe answers and mention as an addendum that they in-universe answers have some flaws).
However, between the phrasing you used in the question, and your subsequent rejection of the technically-correct answer, you seem to be basing your entire question on the premise that this is a plot hole, and you are dismissing the obvious in-universe explanation out of hand. This indicates you aren't looking for an answer (since you disagree with the one given in-universe); you're looking for discussion.
Quite frankly, I think it was a toss-up as to what close reason should be selected:
NARQ: It's difficult to tell what is being asked here. This question is ambiguous, vague, incomplete, overly broad, or rhetorical and cannot be reasonably answered in its current form.
It is difficult to tell what is being asked in your question because you clearly indicated that the simple and obvious answer is not what you were looking for. It seems somewhat rhetorical, since it seems like you are more interested in discussion than in the question your phrased.
Not Constructive: As it currently stands, this question is not a good fit for our Q&A format. We expect answers to be supported by facts, references, or specific expertise, but this question will likely solicit debate, arguments, polling, or extended discussion.
You asked "Why did x happen?". You got the answer "x happened because y". Yet you are taking the stance of "I don't like y as a reason because of a, b, and c... your answer should take into account my arguments". Which is basically soliciting debate and or discussion.
Too Localized: This question is unlikely to help any future visitors.
Of the three, I have to say Too Localized is probably my least favorite, but I think it is still valid. The chances of someone saying "I know they scorched the sky to cut off power to the machines, but that doesn't make sense to me... perhaps stackexchange can help!" are almost nil. Its just too specific, and providing commentary and discussion to go beyond plot holes with clear (if not terribly convincing) in-universe explanations is just not what we're about.
Now, looking at the accepted answer, it seems there is more useful information than the obvious answer. However, the way you phrased your question doesn't indicate that that was what you were looking for.
Which is, I think, the fundamental problem. Your question is pretty clear as to what it is asking, but I don't think, from your subsequent comments, that it really indicates what you want.
Perhaps if the question were something along the lines of:
Why did the humans think scorching the sky would be an effective solution?
Knocking out the machines' primary power supply doesn't seem like it would be worth the cost, since the damage to the environment would hurt humans more in some ways (climate change, food supplies, etc.), and the machines are smart enough to eventually come up with alternative power sources. Was there a good in-universe explanation given as to why scorching the sky was deemed a workable strategy?
