To give my random thoughts on this topic because... Idk, I wanted to.
Can do? Yes, many things are possible.
Would likely do with their stereotypical equipment and training? No, tackling someone as they kill you with a sword isn't a good strategy.
Both naked and only with access to stereotypical knowledge? I'd have to give it to the Samurai. The idea that a martial elite doesn't have at least some skill in unarmed combat is obviously not likely to be that true. And although it's true that humanity as a whole might be healthier/bigger/stronger then we were back then, the martial elite were still in good enough shape that his skill in combat would be the deciding bit. He's not going to be some frail unhealthy thing, even if the Rugby player is in better shape then him it's not going to be by "that much". Especially when optimizing for combat instead of Rugby.
I think in order to finagle a likely win for the Rugby player, you have to change the contest to the point where the operative descriptions of 'Rugby player' and 'Samurai' are no longer the most important ones. If you just say that the Rugby player has a gun, like someone has, well, sure, then he probably wins, but at that point Rugby player isn't the important part of the description, then it's "Dude with gun vs Samurai".
Edit: Of course, one could even go as so far to say that when one says "Samurai" one doesn't necessarily mean the martial elite, maybe what's being described is some sorta bureaucrat or something. But, once again, at least, from my perspective, that seems like it's changing the question. Since. At least to me, if someone says "Samurai" I know they are talking about the elite warrior class from Japan, even if that's not technically the only thing I could get from that question. Subjective, but personally I think most would agree with me.