一旦NUL文字にして、後で戻すとかどう？

str = 'first,second"a,b,c"second,third'
arr = str.gsub(/".*?"/){|m| m.gsub(/,/, "\0")}.split(/,/).map{|a| a.gsub(/\0/, ',')}
p arr #=> ["first", "second\"a,b,c\"second", "third"]