Why did Becket order the Kraken to be killed

Beckett does not have full control over Davy Jones.

He has some leverage, because he possesses Jones' heart (so he can threaten to kill him). But that leverage only gets him so far. Davy has always mouthed off, and has made it clear that he does not like Beckett in any way.

We never see Beckett command Davy to kill the Kraken, we only hear about it after the fact. It's important you observe the context in which Beckett brings this up:

The Dutchman sails as its captain commands. And its captain is to sail it as commanded. I would have thought you'd learned that when I ordered you to kill your pet.

Beckett commanded Davy to kill the Kraken as a show of obedience. This gives Beckett further leverage.

This is karmic justice for Davy Jones. When he was calling the shots on the Dutchman, he pretty much forced Bootstrap Bill to lash his own son. Jones was well aware that Bootstrap would not want the bosun to give the lashings, as he takes joy in stripping away the target's flesh.

Davy Jones made Bootstrap lash his own son, purely as a way to assert his dominance over Bootstrap Bill. In so many words, Davy was telling Bootstrap "you obey me, and me alone. Do not act out against me".

And now, Davy is put in Bootstrap's position, being forced to kill something dear to him because Beckett wants to assert dominance over Davy. In so many words, Beckett was telly Davy "you obey me, and me alone. Do not act out against me".

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.[10] 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.[11] 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.[12] 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.[13] https://en.wikipedia.org/wiki/On_Stranger_Tides

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. http://pirates.wikia.com/wiki/The_Price_of_Freedom