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Use str(datetime.now()):

touch /mnt/sda1/datalog.csv
nano /mnt/sda1/datalog.py

#!/usr/bin/python
# -*- coding: utf-8 -*-
import sys
from datetime import datetime
data_rcv=sys.argv[1] +"," + sys.argv[2] +"," + str(datetime.now())
f = open('/mnt/sda1/datalog.csv','a')
f.write(data_rcv)
f.write('\n')
f.close()

chmod 755 /mnt/sda1/datalog.py

Testing:

/mnt/sda1/datalog.py '1' '2'

ATmega32u4 code:

#include <Process.h>
void setup() {
 Bridge.begin(); // Initialize Bridge
}
void loop() {
 Process p;              
 p.begin("/mnt/sda1/datalog.py");      
 p.addParameter("1"); 
 p.addParameter("2"); 
 p.run();
 delay(10000);
}