I'm aware of the achievements of Sub Saharan Africa - I also know It was a handicapped rather strongly due to the tse tse fly killing of livestock. No livestock means less energy available
There are two parts of this question that need to be addressed. Firstly, the methods of combatting tsetse fly in Africa, and secondly, the idea that it is the "main culprit behind the relative civilizational backwardness of Sub Saharan Africa". I'll start with the first.
In short, Africans across virtually all tsetse areas have had strategies of dealing with the fly long before the twentieth century. John Ford's famous The Role of the Trypanosomiases in African Ecology (1971) actually argued that Africans for centuries had effective strategies of dealing with the fly, and it was the colonial suppression of these strategies (e.g. big game hunting) that led to epidemics of nagana and sleeping sickness in the twentieth century.
There are tonnes of examples of actual control measures, but I will restrict myself to a few. In the 1840s, in what is now Botswana, David Livingstone wrote that the 'Bayeiye' had mentally mapped out local fly-infested areas, and used to take their cattle through these areas at night, a time in which the fly was inactive. He also noted that they would coat the animals in a mixture of cow dung, herbs and milk to create a viscous mixture which repulsed the fly, or trapped it before it could bite them (Livingstone 1857: 80-83).
A second, famous example is 'Mzila's experiment', reported by British entomologist Charles Swynnerton. Mzila, a Shangaan leader in present-day Mozambique, at some point between the 1860s and 1890s instituted a complex 'buffer zone' strategy, where he centralized his subjects and their cattle in a single collective village, and ordered all land surrounding this in a mile radius to be burned to destroy tsetse nests. Soldiers were then stationed in the barren area and ordered to kill any wild animals approaching the village (Swynnerton, 1921). As you probably know, nagana, the cattle disease spread by tsetse fly has a reservoir in African wildlife. The flies are also dependent on wildlife for their blood meals. Mzila's strategy was actually emulated by British entomologists in southern and east Africa (Tilley 2010, Chapter 4).
Thirdly, the word 'nagana' itself is a corruption of the isiZulu uNakane, which is difficult to translate, but is now thought to have meant "continual pestering action" (no doubt referring to the painful bite of the fly). When the Scottish microbiologist David Bruce and his wife Mary Bruce first investigated outbreaks of nagana in now KwaZulu-Natal, South Africa, they learned from Zulu interlocutors that the disease was spread by "big game". These animals (antelope, rhino, lions, etc) were hunted and driven away from agricultural areas to control the disease (Dubow and Beinart 2020, p 184; Brown 2008; Brooks 2001).
Fourthly, according to Clapperton Chakanetsa Mavhunga, Africans along the north and east of the Limpopo river, and also as far north as Mali used what he calls "strategic deployment", "where settlements were positioned in such a way that attackers or invaders encountered the deadly" insects (2018: 31) before reaching the inhabitants. In other words, some Africans actually transformed tsetse fly belts into defensive barriers.
Regarding 'civilizational backwardness', it should be said that this is a value judgement and a colonial stereotype. The absence of large enclosed farms doesn't mean a group of people are 'backward', and 'civilization' itself is a colonial construct. In any case, societies do not all progress in a linear scale from large-scale farming to industrial revolution etc. The idea your question is premised on is a long-standing colonial trope that emerged after the publication of David Bruce's Report on the Tsetse Fly Disease or Nagana (1895) and his subsequent investigations in east Africa: that the fly prevented the development of 'civilization'. Recent scientific studies repeatedly making this argument seem to have forgotten its colonial roots.
There's quite a lot of literature written on this, and I'd highly recommend the following books/theses:
And these articles:
Other works cited in this answer: