… interesting that the US decided to back the “communist” side of the conflict.

Both the US and Libya.

In general, the African Union is concerned that allowing for the redrawing of borders could lead to major wars and displacement of peoples on the continent, moreso than what has already occurred. In this case, the US was likely participating in maintaining the status quo.

It just happened to be that the current government in power was communist, but the US likely thought that preserving African borders was preferable to opening the continent to further destabilization.