From a purely legal perspective, there are rarely 'exciting' biological things that can determine a case one way or the other. This is rather a factor of the rules of evidence in most jurisdiction - there has to be corroboration. To find someone guilty you need to establish the actus reus, the mens rea, and the absence of a defence in as many different ways as possible. It is 'just another' piece of evidence. I'm reluctant to comment on the specific case without having read the case-report, but from a purely legal stand-point, there would be plenty of other evidence. Without establishing that the accused had actually had sex with these women, it would be a possible defence that they contracted it from another source. You'd need to prove this beyond reasonable doubt, meaning that the defence would probably have their own genetic experts to show that this is the most common strain in a given locality. And so on.
One thing that I was working on relatively recently is an example of high-tech genetics being absolutely crucial. We were presented with a man who died of anthrax. This is ... somewhat uncommon. The knee-jerk reaction of the security services was that this was some kind of bioterrorist attack gone wrong! Especially when we found out that the strain of anthrax was a West African one (e.g. not one native to Scotland, therefore one that could have been contracted in the 'normal' fashion). We then dug deeper and could find no links with any terrorist organisation or plot or extremists of any kind. It turns out that our chap had contracted anthrax from an untreated drum-skin. It was therefore a perfectly possible explanation for how we found African anthrax in a small, quiet suburb without any foul play. It was just a one-in-a-million chance kind of thing. Poor chap - he was severely immuno-compromised and what offed him was the drum he played in his support-group meeting.
It is easy to say that the courts rarely get to play with the high-tech toys. The truth is that it all depends on how much money the parties are willing to throw at a given court-case. I've seen CERN physicists advising on radiation matters, leading geneticists on matters of identification, nobel-prize winning physicians on medical causation, and so on.
I would expect that as genetic technologies become cheaper and easier, biotech evidence will become far more common. We can step beyond the often risky science of fingerprint evidence and the always-biased recollection of expert witnesses. Such a development is always to be welcomed - House got it right when he said that people lie. They don't necessarily do it deliberately, but it is rarely the case that a witness doesn't screw something up. This is absolutely to be welcomed in terms of sexual assault. There are few things crueler than the way the legal system currently expects victim-witnesses to confront their accusers. Ideally, we wouldn't have to call them. We have semen samples, we have evidence of bruising, tearing, elevated cortisol levels, and so on. This way we don't have to sacrifice the poor victim's sanity and self-respect in order to nail the attacker.
In this regard, I think the whole CSI-myth is unhelpful. There's a great deal we can do with biotech evidence, but it is a long way in the future that it is all that we can rely on. At the same time, the Court doesn't really cover itself in glory (at least in this country) in the way that they respond to expert evidence - the British courts have explicitly rejected Baysian probability. I'm kind of glad that they have because I've not understood it on the several times it's been explained to me.