These rules will create a lot of debates in the coming days. If one team is to be selected from Asia, it would be India. So no chances for Pakistan, Sri Lanka and Bangladesh team to be in the Olympics. Also if Australia goes to the Olympics, the New Zealand will have no chance and it will be a big set back for them. From Africa, it would be South Africa of course and England will be playing from the European region. One team will qualify through the qualifier tournament and that would be a tough competition indeed.
I would have preferred all 6 teams being selected through the qualifying tournament. For other sports such as football and volleyball, all the teams are selected by such a method. So why give an exception for cricket? And the ICC rankings system can be quite biased. For example, a team like the United Arab Emirates can attain good ratings, because the cricket board is very rich and they have recently organized tours against Bangladesh and New Zealand. On the other hand, teams such as Nepal doesn't have that advantage as their board never receives such offers from the full member nations.
You raised some valid points and concerns for the qualifications for the Olympics but ICC ranking has a special role in the overall cricket infrastructure. Unlike football (FIFA World Cup) or volleyball (FIVB), here in the cricket the full members nations has advantage overall and they have an upper hand as compared to associate nations. The reason is that the overall revenue is generated by those countries and specially the big three nations.
If somehow these full member nations have an early exit or are unable to qualify then it not only hurt their prestige and but impact the financial interests. No doubt ICC Rankings are indeed flawed when it comes to the fairness level. Again the money matters the most and if UAE can spend more money they can have advantage over the other small cricketing nations.