The thing that hamstrings the CG the most is that almost all the CFRs require conviction of a crime. An accusation enough, no matter how credible or accurate is not enough under the CFR to suspend or revoke. The only thing that got him in this case was the alcohol. There is this section of 46 USC:
(d)(1) The Secretary may temporarily, for not more than 45 days, suspend and take possession of the license, certificate of registry, or merchant mariner's document held by an individual if—
(A) that individual performs a safety sensitive function on a vessel, as determined by the Secretary; and
(B) there is probable cause to believe that the individual—
(i) has, while acting under the authority of that license, certificate, or document, performed the safety sensitive function in violation of law or Federal regulation regarding use of alcohol or a dangerous drug;
If there was no reason to believe alcohol was involved the CG would have been largely powerless to do anything. Even when renewing a license, the CFRs require conviction before it can be held against you.
The most difficult procedural issue is I see is the preservation of evidence needed to secure the conviction in court that would predicate the suspension, revocation, or non-renewal of a credential. As soon as the rape happens, the clock is ticking and the ability to get the victim to the appropriate person who can collect the necessary evidence is darn near impossible.
The CG requires non-US flag cruise ships operating in US waters or carrying US passengers to have rape kits on board, personnel sufficiently trained to use them, and a process in place to ensure they can be processed at an appropriate facility in a timely fashion. Seems like something along that line could be explored but expect significant hurdles of all kinds on that one.
The CG is bound by the CFRs and the Constitution, the union is bound by their own by-laws, it seems like the party with the most flexibility and ability to act quickly is the vessel operator.