It also depends on the language, and if you were actually talking about Niger, Africa (even though this should be pronounced ny-jer) or the river in Africa by the same name. Note that in speech you wont be able to tell there was one less g in the word/name. In language niger/negro can also just mean black (as in the color) and isn't at all offensive when speaking in those languages. From Wikipedia (Negro): "The word negro means 'black' in Spanish and Portuguese, from the Latin niger, 'black', probably from a Proto-Indo-European root *nekw-, 'to be dark', akin to *nokw- 'night'."
This isn't any excuse for not thinking when you speak though. For example, there are English words that are not offensive at all in English but if you go to another country they may be very offensive. The same is true for many languages.
All this being said, I have GIMP installed in a pK-12 public school district and no one has ever complained about the name. Its been installed for the last 6 years at least and it does get used.