One of the things I don't see emphasized (forgive me if I missed a post that did) is that, no matter how good or bad ATC, Navaids, Wx conditions, or any other external factors may be, it is the pilot/crew's responsibility to know their aircraft and it's capabilities, and to stay within those capabilities, and to stay within their own personal "envelope" of experience and training.
At first blush, this tragedy seems to be caused by the crew going outside of their envelopes... whether by a corporate culture that allows unqualified crews to operate their aircraft, or by an attitude of TIA (This Is Africa), or any other breach of good sense operational standards.
To add to some that others have said... to say that Africa has to adhere to ICAO standards, is fairly naive. The airspace in any country is owned and administered by that country. If they don't meet ICAO standards (this describes most African countries in one way or another) don't be surprised. Most African governments do things their own way, with little regard to anyone else's opinions or "rules".
As someone with a good bit of Africa flying experience, the presence of ATC, in most situations, is a detriment, rather than an enhancement, of safety... and I long for the "good old days" when aircraft talked to one another on a common traffic advisory frequency, and you were rarely in range of a tower with a "controller" in it!
All of that being said, the TIA factor suggests that this won't change anytime soon, and raises a flag to warn that Afriqiyah should be avoided at all costs in your travel plans.