You may also check the James Boykin papers at the University of Alabama:
http://www.lib.ua.edu/content/findingaids/pdf/mss_0196.pdf

Being captain of a different company, James Hagan probably would not have known what was doing Boykin when he resigned. The record you are attributing to Hagan carries the name Catesby ap R Jones and is dated 1913. Written over fifty years after wartime events, it's not reliable. Anoher post-war roll states that Boykin resigned at Halls Mills AL, which makes more sense.

As for the reason for his resignation, look at 1860 census. James Boykin reported a plantation and slave property worth about $750,000, which makes him one of the wealthiest men in the state. Someone had to be at home to manage the farm and the slaves; leaving home for just a few weeks during the winter of 1861-62 must have imposed a tremendous burden on him. Besides, his wife has several small children and another on the way: she certainly has more than enough to do as a mother, even with a nurse at home.

Many other men with property volunteered but soon resigned like Boykin. Managing an extensive plantation consisting of several farms and 242 slaves would have been a full-time job with little opportunity for other activities, military or business. Boykin may have had some time to be involved in business, but only for brief periods.

Some plantation owners hired managers to operate their land and slaves, but this involved considerable expense and risk.

The University of Alabama register shows James Boykin as a student in the class of 1842. At that time the number of students enrolled was quite small. I count 29 students in this class. Compare this to 219 students in the class of 1864. There is a reference in Hagan's biographical sketch which says Boykin volunteered in Jack Hays' Texas Rangers in the Mexican War.

The reference to surrender at Citronelle AL has confused countless people. What it means is that James Boykin was allowed to surrender under terms granted to General Richard Taylor at Citronelle AL on May 4, 1865. Evidently James Boykin came into Selma on June 13, 1865, and signed a parole which allowed him to return home under General Taylor's agreement.

Another item: the enlistment for James Boykin in the Alabama Senior Reserves shows his age as 46, a resident of Mobile, including notes about his complexion, hair color, eye color and height. He secured a detail within a matter of days as many other planters did and return to prior activities. Being born in 1823, Boykin is too young to be eligible for the reserves. He should have been conscripted and assigned to the army.