I believe that it is meant to be symbolic and ultimately thematic...
On Stranger Tides is actually a novel by Tim Powers. Disney originally had thought about optioning the book during the pre-production of the first film, but ultimately passed until the fourth film.
In 2007, after the successful opening weekend of the third Pirates of
the Caribbean film, At World's End, Walt Disney Studios Chairman Dick
Cook said he was interested in a fourth film. The Los Angeles Times
also reported that Bruckheimer already had rights to a book that could
end up as another installment, though had not confirmed what book it
was. On September 11, 2009, Walt Disney Pictures announced that
the fourth installment would be titled Pirates of the Caribbean: On
Stranger Tides. The announcement had fueled speculation that the film
would follow the plot of the novel. It was later revealed that
while making the films, screenwriters Ted Elliott and Terry Rossio
found Tim Powers' novel and brought it up to producer Jerry
Bruckheimer as an idea to optioned the book for the new chapter.
In a 2011 interview, Tim Powers stated that Disney wanted the film
rights as early as before the release of the second Pirates film, Dead
Man's Chest, though he thought they already used elements beforehand
with skeletal pirates replacing zombies from his book.
However, I have read the novel quit a few times and there are many similar plots/ideas that all the films seem to barrow from it. The reason I think this matters is because then I think Pirates of the Caribbean ultimately may also share themes...
One theme in the novel is this idea that there was once a lot of ancient magic in the world, but over time, man has found it, used it, and corrupted it and so by the novels end it is suggested that there is much less of it, to almost near extinction.
When the Kracken washes up on shore, Jack and Barbossa have a conversation where jack is looking at his reflection in the beastie's eye. Barbossa states, 'The world is not as big as it once was.' and Jack says, 'No, there's just less in it.' (refering to freedom, referring to magic).
I believe this re-iterates this idea that "freedom" is a double-edge sword when it's entangled with magic, because it often requires "power" for one to achieve freedom for oneself (perhaps a selfish act), and so in POTC we have a competition between pirates fighting pirates for magical relics and armies, and ultimately become "cursed" and miserable -- and then with imperial armies and governments dominating the globe and new worlds (Caribbean), from the British Navy to the East India Trading Company to the Spanish Monotheists denouncing pluralistic and/or polytheistic beliefs (destroying the "Pagan" fountain of youth. Implying Magic resides in pluralism/polytheism). In addition I feel certain that the first trilogy set up a redemption arc for Sparrow (Davy Jones Locker = a lack of freedom to move and being "stuck" with a bunch of "useless" selves = escapist/not wanting to deal with himself), as the series now digs further and further into his past and where he is beginning to make-up/atone for his mistakes (ie: Will and Elizabeth).
So I think the idea of Kracken dying is symbolic to the loss of freedom, the abuse/death of magic, and ultimately it's also about the psyche of Becket himself, being "cruel" (and short-sighted) to Davy Jones. It could also be Karma for Jones, as he is also a very cruel person...
Note: DMTNT Post-Credit Scene Suggests Jones is the Captain of the Flying Dutchman again, since it must "always have a captain" -- a kind of Christmas Carol analogy could be made, as they may have to deal with Jones again...
There is also a novel about Becket, Jones, and Jack that takes place in between the junior novels of the young Jack Sparrow Adventures/Brethren Courts and Curse of the Black Pearl titled, The Price of Freedom that gets into the struggle between these three characters.