Word for destroying someone's heart physically
Perhaps there is no really appropriate single word commonly accepted for what you seek, and you should simply use the phrases 'heart removal' or 'heart extraction', which are the terms used on Wikipedia's page on human sacrifice in Maya culture. However, there are terms used in medicine that may be of interest to you.
Mosby's Medical Dictionary lists 'cardiectomy' to mean 'removal of the heart' or 'removal of the cardiac portion of the stomach'. The Miller-Keane Encyclopedia and Dictionary of Medicine, Nursing, and Allied Health lists 'cardiocentesis' as 'surgical puncture or incision of the heart'.
Head : Behead :: Heart : Beheart
There exists a simple English word which stands in the same relation to the heart as behead to the head, and this word is of course beheart.
It uses the privative be- prefix to mean that one is deprived of one’s heart. We also find this prefix used that way in such verbs as belimb and bereave.
Nathaneel Whiting used it in a way that leaves no question as to its meaning. He is explaining the Bible verse 4:9 from the Song of Solomon (also known as Canticle of Canticles).
Cant. 4.9. Thou hast ravished my heart, my sister, my spouse — thou hast behearted me, taken away my heart, as he that hath his head taken away, is said to be beheaded.
The verse he is explaining set in italics (his, not mine) and his explanation of said verse in roman (again his, not mine). That particular text can be found on page 162 of Whiting’s Old Jacobs altar newly repaired, or, The saints triangle of dangers, deliverances and duties, personal and national, practically improved in many particulars, seasonable and experimental : being the answer of his own heart to God for eminent preservations, humbly recommended by way of teaching unto all... published in 1664, as you might have surmised by now. :)
Other writers point out that “behearted” there is a literal translation from the Hebrew. There are many such observances, of which one is from Thomas Brooks on page 359 of his A cabinet of choice jewels, or, A box of precious ointment, etc, published in 1762:
‘Thou hast ravished my heart,’ (or thou hast behearted me, as the Hebrew runs) ‘my sister, my spouse;
Wiktionary gives a definition for this word as meaning to enamour or to ravish citing Thomas Brooks as reprinted in 1866, plus another citation by a different author two years later.
The word "decardiate" has been used at least once before, presumably by analogy* to "decapitate."
This word apparently occurs in Conan of the Isles (1968), by L. Sprague de Camp and Lin Carter.
It's mentioned in the following review by Ryan Harvey, who doesn't think much of the word:
In places, their word choice falls flat or else strains too hard to grasp an obscure term. I have never seen anyone use the word “decardiate”—to remove the heart—in a work of fiction before, and I doubt I will see it again.
*I think the analogy is not entirely legitimate, however, because capit- comes from the Latin word for "head," caput/capitis, while cardi- comes from the Greek word for heart–the Latin word for heart is cor, cordis. Cor is the nominative and accusative form: derived words are typically built on the stem cord-, which occurs in the English words accord, concord, discord, record, cordate, obcordate. So theoretically the "heart" equivalent to decapitate would be "decordate" but all the results for this on Google are misspellings of the word "decorate".
There are actually some interesting Greek verbs derived from the noun καρδία that seem to have an appropriate meaning, such as καρδιουλκέω kardioulkéō "draw the heart of the victim at a sacrifice" (also apparently a synonym καρδιουργέω kardiourgéō) and ἐκκαρδιόω ekkardióō "cut out the heart", but unfortunately there is no generally established way of adapting Greek verbs into English ones.
From Aztec Sacrifice. Post-Conquest Nahua Painting, c. 1560...
The Aztecs carved the heart out of an alive human war captive, dedicated his heart's blood to the sun, and ate his body in order to honor their gods and to preserve the world...
...
...THE EXCARDIATED VICTIMS WERE FLUNG DOWN THE STEPS OF THE PYRAMID
(Sorry about the CAPS - they're in the original)
Obviously we don't often need such a term (and no - it's not in the full OED), but the above strikes me as as both easily understood1 and unremarkable (so no need for "scare quotes").
1 Most native speakers will be familiar with cardi- (relating to the heart) from words like cardiac arrest, cardiovascular disease, cardiogram. And the relevant senses of prefix ex- (away from) and suffix -ate (used to create a verb form) are reasonably common, so given even minimal context, this "neologism" should be reasonably transparent even on first encounter.