Yes, you have got the gist of it.
Scrub here means scrubland (see the second picture on this page http://www.theguardian.com/global-de...ion-saferworld)
I have explained the sentence, which hopefully clarifies why you are thinking along the correct lines.
Some of us tried to open up the Soudan [to British trade and colonial expansion in the late 19th century, but got more than they bargained for] and [they] were opened up by Fuzzies [literally opened up by the blades of the native army. It should be noted that Kipling uses a pejorative term, commonly used in his time, to describe the native inhabitants. This term is very definitely not acceptable nowadays, but was a feature of writing and speech of that era.] in that cruel scrub outside Suakim [in that harsh scrubland outside Suakim].
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