If a Soldier is pending UCMJ, could that stop them for getting approved for an AER loan?

AR 930–4 ch 2-6
if the UCMJ will result in discharge, aid is limited to basic needs.
Family members also eligible limited to basic needs.

AER is doled out based upon command support and the need as identified by the Service member. I do not see why the command would pour fuel on the fire by withholding support that was identified as a critical need.

However, if your issue is likely to result in separation that would give the command pause to supporting the loan.