Raúl Vera, the often-controversial bishop of Saltillo, claims that the death of Arturo Beltran Leyva was an"extrajudicial killing" on the part of the Navy. He says the boys in blue had no intention of capturing the narco, and swooped in on the Cuernavaca complex with intent to kill.
If this is true, the Mexican military has some explaining to do. Narco he may be, but Arturo Beltran Leyva has rights just like the rest of us. In this war on drugs, if the military can kill a high-level suspect without repercussion, what's to stop them killing a low-level one? More than 80,000 people have been locked up in the war on drugs since Calderon took office – how many of these men and women had their rights waived? What if the policy had been shoot to kill – would they all be lying in mass graves right now?
Back to the Navy and its intent to kill Beltran Leyva. I don't have any sources in the Navy, so I can't vouch for the accuracy of my next statement, it's speculation.
But yes, the Navy did go into Cuernavaca with the intent to kill Beltran Leyva. Although extradition proceedings have improved between US and Mexico, jailing a top narco like Arturo BL is too risky; all evidence against them may not hold up in a court of law, particularly in a US one. (There's currently one narco who is desperately seeking extradition to the US, because he firmly believes that evidence against him would be thrown out by a US court; in Mexico, he'd get at least 20 years in a maximum security facility)
Former DEA officials have told me that there is literally no interest in capturing guys like Beltran Leyva and Chapo. Killing them is the only way to bring them down completely.
It's not quite the Escobar era in Colombia, when the U.S. was actively working to kill the Medellin drug lord, but the same intent is there.