I was able to remove the frameworks in the PlugIns folder via a Run Script build phase (specify the path to each framework in input files - $(BUILT_PRODUCTS_DIR)/$(PLUGINS_FOLDER_PATH)/Binary.framework):
#!/bin/bash
COUNTER=0
while [ $COUNTER -lt "${SCRIPT_INPUT_FILE_COUNT}" ]; do
tmp="SCRIPT_INPUT_FILE_$COUNTER"
FILE=${!tmp}
echo "Removing $FILE"
rm -rf "$FILE"
let COUNTER=COUNTER+1
done