Well, there's two likely scenarios:
(1) The Vasudans were acting under orders from Vasudan High Command, in which case they would probably quietly be shuttled back to the PVN to lead the rest of their lives in early retirement, in exchange for not making any disunifying comments against the PVN.
(1) Definitely gives the possibility for a lot of controversy, as Terrans would see the Vasudans going home to their families while one of their own was held up as having participated in a shameful act. Furthermore, the lack of testimony by anybody other than GTA personnel would give an unsatisfactory verdict. With the PVN likely backing the GTA on keeping the mysteries of when the Shivan's appearance became clear, you can bet there would be a lot of discontent.
(2) The Vasudans, too, were renegades and were most likely elements of the HOL. However it does seem a bit of a misnomer to call them part of the "McCarthy Trials" if this were the case. There would be far more HOL-related court martials than McCarthy court martials. While they might be put on trial to offer testimony, their testimony would likely be regarded with great skepticism given their anarchial leanings. The PVN would almost certainly insist on a court martial, and based on the impression of the Vasudans in Freespace 1, I'd guess it would have been swift, decisive, and not very public.
If it were (2) though, it would be an open and shut case.
(3) The status of the Vasudans on board the Rasputin wasn't known because they became MIA/KIA during the remainder of the armed conflict in that era. Despite this, prosecutors made the case that the Vasudans were HOL operatives, despite the lack of solid evidence, and McCarthy was still convicted.
Lack of concrete evidence, potentially unfair tactics by the prosecutors, and a strong possibility of Vasudans feeling slighted and lots of discussion and possibly some kind of protests or interspecies violence-a very good candidate. Plus there'd be the many people convinced that the GTA had killed the Vasudans themselves, secreted them away, or otherwise prevented them from being capable of offering any testimony during the trial.
Just based on how Lt.Samsa states it, I'd guess that it's something like #1. The Vasudans were released back to the PVN and possibly provided some testimony at the "McCarthy trials", which consisted of individual trials of McCarthy and his crew. During this time, insinuations that the trials were being used by either or both the PVN and GTA to weed out people from the ranks that they thought were objectionable in some fashion came up. During the trial, evidence that the GTA did indeed know about the Shivan attack on Ross 128, long before it alerted anyone else, came to light and began circulating in the media. Many people began to sympathize with McCarthy and his crew. However, the court martial found McCarthy guilty of high treason during a time of war and had him executed. The majority of the other individuals were convicted and sentenced to long prison terms. However, in the intervening years and with the chaos following the GTI rebellion, additional information came to light that proved that many of the people sentenced had been innocent.
For many civilians, this became a question of whether a Lt. had the right to take action where the GTA High Command failed to take the appropriate action. It became widely discussed in ethics circles. However, among military personnel, and served as a hallmark case representing the lesson needed to be learned about understanding one's place in a military hierarchy. There's a similar theme in
Starship Troopers. Hence, to Lt. Samsa, the trial serves as an important part of recent military history and is a good thing - it keeps idiot recruits from thinking they can thumb their nose at their CO. To pretty much everyone else in the GTA, the trial was a source of temporary indignation and frustration at their government, and representative of the failures therein (eg the economic collapse by the Terrans alluded to in FS2).
So when Lt.Samsa says they were a part of history, he's not kidding.
The McCarthy trials were probably one of the last big events before the GTA went bottoms-up.
'Course there could be something even more malicious at stake here. It could be that the GTA tried to pin some or all of the blame for instigating the Shivan attack on McCarthy, and turned him in to a pincushion for people whose anger was directed at the GTA for the death of loved one(s). Thus Lt.Samsa would be justified in having a "justice served" attitude, but he'd have no clue what he was talking about. Kind of fits with the cloak-and-dagger theme of FS2.