1. "Net neutrality ensures network operators don’t discriminate by limiting access to services you want to use." - in a country where there are huge economic obstacles to connectivity and the internet is not affordable to everyone, offering certain services for free automatically discriminates against the services that are left out since they are not deemed to be "essential" by the government or local mobile operators. Also note that these countries don't have the most ethical of the governments (yes, I'm from India and have seen how the government works pretty closely), and mobile network operators are ultimately responsible to the share price of their stock, not the overall social welfare of the country.
2. "Internet.org doesn’t block or throttle any other services or create fast lanes -- and it never will." This is true, but if one looks from a slightly different perspective, free lanes are as bad - maybe worse - than fast lanes. One has to admit that internet.org is ending up creating free lanes for certain services, in a country where the toughest obstacle to internet connectivity is not lack of availablity of mobile network infrastructure, but the economic situation of the country's poorest poor.
Like with all tough cookies, the solution doesn't lie in suggesting that this is better than nothing. It lies in admitting to the apparent problems in the internet.org ecosystem (clear lack of net neutrality) and working out the answers. A solution lies in offering the internet as a whole for free upto a basic data usage (limited by bytes, not services), working on innovations like the low flying drones or loon style projects which place mobile internet infrastructure in places where there's none (I know internet.org is already working on this), working on business and technical innovations to enable the mobile operators offer better, faster and cheaper services to more people and finally, working on faster, cheaper mobile devices. ($50 is not cheap enough in a country where median per capita income is as low as $616 (2013) - in comparison, the same figure for US is around $26k)
I understand internet.org was founded by Facebook to connect the remaining 4 billion - and it's a very noble initiative. But we have to be very careful of the long term.