You could just replace those commas within the quote with some other string or remove them if you wanted with some awk or sed. Here is a somewhat relevant example from stackoverflow:

awk -F'"' -v OFS='' '{ for (i=2; i<=NF; i+=2) gsub(",", "", $i) } 1' infile

1. https://unix.stackexchange.com/questions/48672/remove-comma-...