To understand the climax, you got to recollect the begining. When Mugil reaches the hospital he blacks out, and the upside down camera cuts to the title card where clouds swarm in the sky. Here, Mugilo Megamo is just a title song. Soon after, he wakes up and the story unfolds.
Towards the end, he accepts to be with Megha and kisses here forehead. Following it, they are in white dress under a white umbrella (Similar dress they wore during their first meeting). After a few candid shots of them together it cuts back again to the clouds swarming the sky. Here the song Mugilo Megamo has entirely a different meaning and tone altogether.
"
mugilo megamo sol veru veru
irandum irando porul onru thaane
udalal thegathaal irandaana pothilum
uyiraal unarvinaal athu onruthaane
neeyo naano iru jeevan onre
"
So, initially he was thinking of Megha and finally too he is thinking about Megha. Megha is still in Coma, but she lives, smiles and laughs just like the wide spread clouds which are always with him and above him.
There are 2 clues :
1. After that head surgery, she cannot have grown that much of hair in just "Few Months"
2. The caption is not the same font - initially in the movie September <date> is entirely a different font than the end "Sila mathangalukku piragu". My guess is that, its the producer cut which included it to give a "happy-go-ending" to the movie, and I strongly beleive Karthik Rishi had thought otherwise which is indeed the best ending possible where you travel back with the song Mugilo Megamo banging your head.
And about the (revenge)murder he commits, well, its an open ending. He may be in jail or Megha is no more or he was escaped by Jayaprakash etc., But the underlining point is that Mugil is so much in Love with Megha that he virtually starts living with her. Vijay Kumar had the same syndrome (It is said by Jayaprakash that Vijay Kumar asks his (dead) wife to serve coffee), so does YGM and now Mugil. So all the 3 had similar feelings, voices and visions - I suppose the main theme of the movie.