Before 2010, they didn't used to get hijacked like that despite the risk. There was a bit of a gentleman's agreement about organizations like MSF, UNICEF, and the GPEI. These sorts of NGOs got a lot of access in many countries because they were "off-limits" for espionage.

There's not a terrible chance (although I would give it less than a coin flip) that the CIA hasn't developed any assets in any of these medical NGOs since then, but the illusion has been shattered with the one incident.