> Can't they just help more directly to eradicate polio instead of paying a corrupt government to do it?
That's not how any of this works. You don't just go to a foreign country with its established health care system (and national sovereignty) and start building seperate health care structures through your NGO without government approval and ownership.
What you do instead is build broad alliances between the government, international donors and implementing agencies (which may include foreign NGOs). Financial and programming oversight is performed jointly by all partners.
This particular Japanese loan was part of broader international funding for Nigeria's National Polio Eradication Programme. The money was channeled to UNICEF and WHO to procure Polio vaccine and to improve related health care services in the country. The involvement and leadership of the Nigerian government is crucial to make sure you have political legitimacy and to create sustainable policy change and improvements in the national health care system.
Payments like these can be interpreted as buying a state's benevolence (aka corruption), something that Soros is regularly accused of.
I'm sure there are quite a few NGOs that are more efficient in fighting polio than the Nigerian government.
Likewise, should we pay Kim Jong Un to feed hungry North Koreans if it were possible to send them food directly?