Skirmishers are incredibly effective at early-game defense. Many defensive weaknesses of the Archer are solved by a higher combat strength.
With a higher defensive ability, fewer Skirmishers need to be built to have the same impact as Archers. This allows more focus on development.
A Mali player may very well keep off researching Longbowmen longer than other players to focus on building Mints, developing religion (as Mansa Musa is a Spiritual leader) or suchlike - Mali's set-up means that they have multiple priorities at this stage of the game. As such, they can be hit while Mali is focusing on more peaceful techs.
Against Skirmishers directly, mounted units can do fairly well due to their higher combat strengths. Giving Swordsmen the Cover promotion can also be effective.
For Skirmishers in cities, just make sure you have plenty of Catapults to weaken cities before overwhelming them. Mali isn't any better at crushing stacks than other nations, so go ahead and send some.
At its height, the Mali Empire stretched halfway across Africa, and included many subordinate tribes. To keep order, the Mali employed a huge standing army. During war, the Mali often fought as "skirmishers" - soldiers who fan out in loose formation to protect the main force's flanks or front. The Mali skirmishers were lightly-armed archers in that force, famed for their courage and their marksmanship.