Initially, the Malians were a fast civilization with a great economy and a large array of viable military options. Testing proved that they did not have a true weakness and were difficult to counter because of their speed and economic power, particularly in the castle age. The two economic nerfs that you mention were designed to curb that.
The loss of halberdier was meant to mitigate two main concerns:
1) Early-imperial halb-ram pushes. Not unlike Vikings, it was often the case that Malians could enter the opponent's base with capped rams and another imperial age unit while the opponent was still in the castle age. Malians could do this, and their halberdiers had 7 pierce armor on top of it.
2) Having such high pierce armor on their barracks infantry allowed Malians to field an extremely inexpensive lategame army of champions and halberdiers that countered pretty much everything unless the opponent had much more gold, an anti-infantry UU, hand cannons/slingers, or an infantry bonus of their own. Unlike Goths (to whom this is perhaps most comparable), they did not lack plate mail and did not need a castle and unique technologies to reach this point.