Generally, the concept of מלאכת מחשבת which we learn out from the mishkan as being necessary to be chayev on shabbos, limits the accountability for violating shabbos. For example, the reason that we exempt a מלאכה שאין צריכה לגופה and mekalkel are all based on the fact that they are not considered mileches machsheves, therefore one is not chayev for them on shabbos (to the exclusion of דבר שאינו מתכוין אליבא דר"ש which is an exemption in kol hatorah kula as we see from many gemaras). However, in our gemara the concept of mileches machsheves is used to explain why one would be chayev for winnowing on shabbos, even though the wind is necessary to assist in the melacha which for damages would not make him liable. How can the rule of מלאכת מחשבת be used as an exception sometimes to be machmir and sometimes to be more meikil that kol hatorah kula?
The Even Ha'Ozer (O.C. 328) discusses using a leach to draw blood on shabbos, whether it is a Torah violation of making a chabura, or since the actual chaburah is being done by the leech itself, the person is not chayev. Although he rejects the proof of the Magen Avrohom, he cites his own proof that one would be chayev. He introduces this with a question: We find that one is allowed to put his animal on the grass on shabbos, knowing that the animal will eat. Yet, when one is ma'amid his animal on the produce of someone else, he is considered a mazik and chayev for damages. If in the context of damages we consider it an action not just a grama, he should also be chayev on shabbos? He rejects the notion that one is more likely to be chayev for damages, based on our gemara where we clearly see that one is more likely to be chayev for shabbos than for damages? He concludes that shabbos is not more kal or chamur than nezikin, rather they are dependent on different factors. For nezikin the primary issue is whether the damage will be definite - so long as the damage will definitely occur, whether it is with his intent or not, it is considered an act of damage not just a grama (therefore one is chayev for standing an animal on his friends property to eat). But in the context of shabbos, מלאכת מחשבת אסרה תורה, meaning that the primary factor is that he intended to violate shabbos, and succeeded in shabbos being violated, therefore even if the result is definite he will be exempt so long as that was not his intent. But, when that is his intent such as in our gemara where he intends to winnow, he would be chayev even though the wind assisted him. The same would apply to a leech, since his intent is that it make a wound to draw out blood.
Based on this, מלאכת מחשבת doesn't make shabbos stricter or more lenient, just different. On shabbos the entire focus is whether his intent was to result in the melacha, therefore even if he required so assistance from the wind he would be chayev. But when there is a lack of intent such as מלאכה שא"צ לגופה he is patur.