One of the key reasons I support MSF is because I think they are very principled.  One of the pitfalls of working in war zones is that it is a political mess, and many people will try to extract a portion of the monies in the form of "commission" or bribes.  Your charity might LOOK like it spends 80% of the money you donate it on charitable work but is it really getting to the people that need it? 

It's an ethical stance to take, and not all will agree with it, but MSF will pull out of countries and areas where this practice is in place.  Many other charities take the view that this is a cost of doing business and it would be better to get 40% of the money to the starving, dying people than none at all.  They may accept the theft/siezing of some of their supplies in order to get the rest through.  Personally, I do not take this view, and it appears neither do MSF.  Money (and in their case, medical assistance) is a scarce commodity and can be used in many locations across the globe. If they feel it can be used to better effect elsewhere, then they will pull out.  This also has the benefit of refusing to reward corruption, which is a good thing I think.  It's also a benefit of being a global organisation - if you are a charity only operating in one country, you're sort of stuck with the corruption regime there.

It's the same sort of argument over whether on principle to pay a kidnapper's ransom I suppose.  So it depends on your view but I think it should help you make an informed decision.