After initial hiccups and weird experience (Gmail booking tickets) with MakeMyTrip and Go Air, am pleased to share that This story seems to end with a happy note, heres the status
MakeMyTrip
1) There were few mail exchanges
2) Some interactions with call center reps
3) They have promised to send a cheque ( in next ten business working days) for reimbursing the full money for alternate flight i got booked on 3rd April. (So this cheque along with refund of Bombay to calicut flight amounts to full refund)
GoAir
1) They sent a redeemable voucher of Rs 2525 with six months validity. I am not too sure how this number was calculated.
2) No further communication from them so far. (and i dont think there is any need, now)
Interestingly, they are not learning
For my return flight, there was again discrepancy in timing, this time actual departure time was 20 mins postponed. ( from 1510 hours given on e ticket to 1530 hours). Again it was GoAir ticket booked via MakeMyTrip. This time i mailed GoAir people to inform me if there is any change in timings. They did called up before flight time and informed me about the new timings.
Interestingly I had to ask them for the same. Neither MakeMyTrip nor GoAir people cared to do the same on their own. No message, No mail, No call. This is interesting, to note that they are not learning their lessons
Seems like they want to make a society of responsible consumers 
at least i have learned my lessons well
Questions
1) As a friend of mine suggested you might get the money, but what about mental harassments?
2) There is either bad or no communication between MakeMyTrip and GOAir as they both are returning money and Voucher respectively. I might end up getting more than I spent (Extra money for mental Harassment). Hope they look into it and sort things out or shall i bring this to their notice?
3) Not too sure if MakeMytrip giving money on their own or they taking refund from GOAir?
Lets hope they send the money…
