So my first question is, what is your criteria or framework testing your hypothesis that "the Trans-Sahel Counter-Terrorism Partnership (TSCTP) is too heavily militarized and, thus, insufficiently civilian in nature."

Your thinking begs a number of questions:
What is the proper balance?
What criteria should determine that balance?
How is this program resourced currently?

The bigger issues you hit later are common themes from DoD, going back to the SecDef's speech at Kansas State in November 2007. I would not say that DoD ended up in this space through 'no fault of its own' but there was a lot of white space for them to move into.

As far as a paper goes, you might want to evaluate how TSCTP might be otherwise/ideally resourced, in light of AFRICOM/evolving DoD/State/AID priorities and strategies (DoD Quadrennial Roles and Missions Review, the US Govt Counterinsurgency Guide, etc.).