This could be out of date, but anything in the military can be waived by someone, and I’m sure Obama himself would authorize it to show his support for gays, if needed:
26 AR 165–1 • 3 December 2009
8–9. Loss/change of ecclesiastical endorsement
a. All Chaplains are required to have on file with OCCH an Ecclesiastical Endorsement (DD Form 2088) submitted
for them by an AFCB Listed Endorsing Agent. If an Endorsing Agent withdraws a Chaplain’s ecclesiastical endorse-ment, then the officer must immediately cease from all religious activities, that is, performance of rites, ceremonies,
services, pastoral counseling, and so forth. Under no circumstances will the Chaplain perform any Chaplain functions without a valid ecclesiastical endorsement.
b. A withdrawal of ecclesiastical endorsement is official when a Chaplain’s Endorsing Agent notifies the CCH of
the loss of endorsement in writing. In accordance with DODI 1304.28 and AR 600–8–24, the CCH will then notify the
Chaplain of the loss of endorsement and offer the following 4 options:
(1) Seek a new ecclesiastical endorsement from an AFCB Listed Endorsing Agent. If another ecclesiastical endorse-ment is not obtained, the Chaplain will undergo involuntary separation in accordance with AR 600–8–24 or AR
135–175.
(2) Submit a voluntary retirement request, if eligible.
(3) Submit an unqualified resignation request. If the Chaplain has not fulfilled their MSO, then the request is
forwarded to the ASA(M&RA) for waiver approval.
(4) Request a branch transfer. If a Chaplain is granted an appointment in another branch, the officer will not wear
the Chaplain branch insignia or be assigned to a Chaplain position.
c. Chaplains seeking a change in ecclesiastical endorsement must submit a request to OCCH, DACH–1 and coordinate the action with both current and prospective Endorsing Agents to avoid a loss of endorsement. As the approving authority, the CCH may convene a special advisory board to review the circumstances surrounding a Chaplain’s request for a change in ecclesiastical endorsement.
Thanks, Mr Rogers, the bold and underlined section above is the part to which I made reference.
The losing endorser CAN block it. It must be coordinated.
Given that, my suspicion is that the SBC acquiesced, so it's on them. That Colonel had more than enough time to retire handsomely AND enable the SBC to demonstrate that it stood behind its principles.