How old is your son? I think based on what Im reading here:
http://www.army.mil/usapa/epubs/pdf/r40_501.pdf your son's condition may indeed be disqualifying factor.
If your son is on prescription medication for his GERD he should be sure to maintain as prescribed and not let it run out.
2–3. Abdominal organs and gastrointestinal system
a. Esophagus. Current or history of esophageal disease, including, but not limited to ulceration, varices, fistula,
achalasia, or Gastro-Esophageal Reflux Disease (GERD) (530.81), or complications from GERD including stricture, or
maintenance on acid suppression medication, or other dysmotility disorders; chronic, or recurrent esophagitis (530.1), is
disqualifying. Current or history of reactive airway disease associated with GERD is disqualifying. Current or history
of dysmotility disorders, chronic, or recurrent esophagitis (530) is disqualifying. History of surgical correction for
GERD within 6 months is disqualifying. (P42 esophageal correction, P43 stomach correction and P45 intestinal
correction.)
b. Stomach and duodenum.
(1) Current gastritis, chronic or severe (535), or non-ulcerative dyspepsia that requires maintenance medication is
disqualifying.
(2) Current ulcer of stomach or duodenum confirmed by x-ray or endoscopy (533) is disqualifying.
(3) History of surgery for peptic ulceration or perforation is disqualifying.
c. Small and large intestine.
(1) Current or history of inflammatory bowel disease, including, but not limited to unspecified (558.9), regional
enteritis or Crohn’s disease (555), ulcerative colitis (556), or ulcerative proctitis (556), is disqualifying.
(2) Current or history of intestinal malabsorption syndromes, including, but not limited to post-surgical and
idiopathic (579), is disqualifying. Lactase deficiency is disqualifying only if of sufficient severity to require frequent
intervention, or to interfere with normal function
(3) Current or history of gastrointestinal functional and motility disorders within the past 2 years, including, but not
limited to pseudo-obstruction, megacolon, history of volvulus, or chronic constipation and/or diarrhea (787.91),
regardless of cause, persisting or symptomatic in the past 2 years, is disqualifying.
(4) Current or history of irritable bowel syndrome (564.1) of sufficient severity to require frequent intervention or to
interfere with normal function is disqualifying.
(5) History of bowel resection is disqualifying.
(6) Current symptomatic diverticular disease of the intestine is disqualifying.
d. Gastrointestinal bleeding. History of gastrointestinal bleeding (578), including positive occult blood (792.1) if the
cause has not been corrected, is disqualifying. Meckel’s diverticulum (751.0), if surgically corrected greater than 6
months prior, is not disqualifying.