With the knowledge that an opposing force was approaching your position, the commander of the confederate forces had two choices:
(1) Transport the sick and wounded, as well as possible, or
(2) Abandon them to be captured.
Sibley, on his flight back to San Antonio, chose the latter. You can make the case that it was the "humanitarian" choice, or I can make the case it was the "expedient" choice. Either way, they were left behind.
His position? The only time Carlton ever came even remotely close to Sibley's position was a brief skirmish near Tuscon. Sibley left because of Canby's actions in New Mexico, not Carlton's in Texas, and was well out of Carlton's way when his forces made it back to El Paso that May. Carlton was still running around somewhere in Arizona or western New Mexico at that time and did not make it to El Paso until August - four months after Sibley returned there and almost two months after Sibley's rear guard pulled out to San Antonio! To suggest that Sibley was running from some sort of imminent attack by Carlton - so fast that he allegedly didn't have time to bother with the wounded - is accordingly outright absurd.
the commander of the confederate forces had two choices: (1) Transport the sick and wounded, as well as possible, or (2) Abandon them to be captured.
Garbage! Why would he see some imminent need to transport them in June? Sibley did not know if Carlton was even going to head for El Paso considering that Carlton was a state away at the time of the pullout and considering that their forces only met once in a single skirmish outside of Tuscon. They were safe in El Paso and probably could have easily held off any attack by Carlton had they decided to stay, but that would have been strategically stupid since the war was for the most parts over in New Mexico and West Texas was of no strategic value.
Ockham's razor is simply against you on this one, capitan. Far from being the product of a convoluted botched exit strategy, the simplest explanation - that being the health threat posed by desert travel in the middle of summer - is the most likely.