#+BEGIN_SRC emacs-lisp :results silent
  (defun group-number (num &optional size char)
    "Format NUM as string grouped to SIZE with CHAR."
    ;; Based on code for `math-group-float' in calc-ext.el
    (let* ((size (or size 3))
           (char (or char ","))
           (str (if (stringp num)
                    (number-to-string (string-to-number
                                       (replace-regexp-in-string "," "" num)))
                  (number-to-string num)))
           (pt (or (string-match "[^0-9a-zA-Z]" str) (length str))))
      (while (> pt size)
        (setq str (concat (substring str 0 (- pt size))
                          char
                          (substring str (- pt size)))
              pt (- pt size)))
      str))
#+END_SRC

The following code block will call the group-number Emacs Lisp
function on every cell in its input argument which is a number.

#+name: table-number-grouper
#+BEGIN_SRC emacs-lisp :var data='()
  (mapcar (lambda (row)
            (if (equalp row 'hline) 'hline
              (mapcar (lambda (cell) (if (numberp cell) (group-number cell) cell))
                      row)))
          data)
#+END_SRC

Here's a simple shell code block which produces the table (this is a
stand in for your R code block).
#+begin_src sh
  cat <<EOF
  100000000.55    a
  23000   b
  3000    c
  40004   e
  5000    3
  EOF
#+end_src

#+RESULTS:
| 100000000.55 | a |
|        23000 | b |
|         3000 | c |
|        40004 | e |
|         5000 | 3 |

Above is the poorly formatted output of your block.  Below we add the
"post" header argument to your block, which will use the
"table-number-grouper" code block above to post-process your results.

#+begin_src sh :post table-number-grouper(*this*)
  cat <<EOF
  100000000.55    a
  23000   b
  3000    c
  40004   e
  5000    3
  EOF
#+end_src

#+RESULTS:
| 100,000,000.55 | a |
| 23,000         | b |
| 3,000          | c |
| 40,004         | e |
| 5,000          | 3 |