According to Chris Peers, even the regulars didn't stay uniformed for long. It seems they soon abandoned wearing their smart white uniforms on campaign once in Equatoria (they liked to keep them for best), and would have more the appearance of some of the ragged askari from the Foundry DA range. Typically they wore brown shirts, apparently.
Baker recruited Madi tribesmen to help fight the slavers, so you could use Foundry naked spearmen for them. His red-shirted "Forty Thieves" created such a reputation for their fighting prowess that many Egyptian/Sudanese troops in the region acquired and continued to wear red uniforms, hoping it would instill fear in their foes. In his Foundry book on East Africa Peers doesn't make specific mention of irregulars, but he has Bazingers and others in his Egyptian army list for the "In the Heart of Africa" rules.
You could use the Foundry Wangwana-style askari as irregulars, also conceivably the Zanzibaris would fit, too. Also, the Perry Bazingers are perfect for irregular troops of the region:
(These could equally be used to represent the slavers that plagued the Madi, Bari and other tribal peoples.)