Follow the money. Just like Make-A-Wish stopped funding hunting trips for terminally ill children due to pressure from their benefactors I'm sure that the vast majority of contributors to the ACLU are of a left leaning political bent and the ACLU is worried that taking on 2A cases would negatively impact donations.
The ACLU is willing to sell out one section of society in order to keep the $$ rolling in.
Always follow the money.
Bronson