Someone said in an early post on this place that women samurai were highly unlikely, and I read that, and was pretty sure I've read stuff contrary to that point some years ago, so I thought I'd go look it up again. Basically, women of samurai families did in fact receive some sort of martial arts training. They weren't expected to go into battle like their men (at least, not in later periods), but were responsible for the majority of noblemen's household tasks, including supervising harvests and watching the coffers. The noblewomen were also usually armed with (hidden) daggers, mostly for defense of honor reasons; that is, to defend themselves from someone trying to damage their reputation, or, in the event their reputations were damaged, commit suicide. And yes, they were trained to use those things in lethal ways. Those who've watched the first Rurouni Kenshin OVA (and the Kyoto Arc of the series) might remember that Tomoe carried around a dagger, as did Yumi (the oiran/courtesan from the Kyoto Arc, hope I remembered her name right).
There were actual women warriors from samurai families fighting alongside their men in early Japanese history, even ruling (if I'm not mistaken, someone correct me if I'm wrong, but wasn't the Chrysanthemum Throne founded by a woman?). Noblewomen were trained in the martial arts well into this century, and did use weapons, just not exactly the weapons (link goes to a good gallery of recognizable weapons from Rurouni Kenshin and PMK) samurai men used. I remember reading Geisha of Gion, and there was a mention of the author's grandmother (of noble blood) being a skilled martial artist; it was a book mostly about geisha, but the point is that martial arts skills were taught to women of noble families well into the 1950s. The role of women as actual soldiers, however, seemed to have dwindled with the introduction of Confucianism and Buddhism into Japan. This trend does seem to follow what happened in ancient China, where women of at least the pre-Qin dynasties were known to have been soldiers, even generals, fighting alongside their men (there was a famous concubine-general from the Spring-Autumn period, name eludes me though). Even then, they did have powerful roles as religious leaders (Kikyou the Miko, anyone?), one lady, Hojo Masako, even going so far as to take the reigns of power from her husband, the first shogun of Japan.
As far as geisha assassins go, however, I believe that to be rather unlikely. I could be wrong, if anyone has documentation on this, please do let me know, I'd be very glad to learn. Geiko did play active parts protecting their warrior lovers (be they Choushu or Shinsengumi or anyone else), particularly towards the end of the Tokugawa era. Some geisha were trained in martial arts, this seemed more for fitness reasons, however--one of them being the very famous Sadayakko. But, as Lesley Downer describes the geisha of the Tokugawa era in "Geisha", "When the shogun's crack troops came marching through Gion, conducting house-to-house searches, it was the geisha who confronted them, arguing with them while their lovers hid in closets or on false floors under the tatami matting or sneaked away out of back doors. Some of the geisha were threatened or even tortured but they would never give away the rebels' hiding places. At least they were able to stall for time, to give their lovers the precious few extra minutes needed to make their escape." Someone did mention earlier somewhere that this had to do a lot with the geisha's general code of secrecy with regards to their clients (and non-clients, as it sometimes were), which I agree with.
Okay, now for some mad fun with Okita "He's not a girl!" Souji. It has long been the history of warmongering ancient civillizations to idealize male-male love, seeing it as a sort of perfect love, compared to the more "corrupted" male-female love. This seemed to have a lot to do with the bonds of men who fight together on a daily basis. It went all the way back to ancient Rome, where the theory was apparently that men whose lovers who went down in battle fought harder. And it was also apparent in ancient China, which even had boy-marriages (also includes lots of lovely poetry) for the common people at one point. So we come to...nanshoku, "the love of the samurai." Which, in those days, well and truly wasn't wrong either.
For those who'd rather not read the essay at the link above, these are the lines worth noting: "In some important aspects the traditions diverged: in Japan the youngster was expected to make the first advance, while the Greeks held that it was proper only for the man to court the youth....A young man should test an older man for at least five years, and if he is assured of that person’s intentions, then he too should request the relationship… If the younger man can devote himself and get into the situation for five or six years then it will not be unsuitable.”
Of course, this in no way means the real Okita Souji was into other guys. And the essay does sort of say that the practice of samurai love was dwindling by the Tokugawa period, in any case. But it can, or might, explain the Okita Souji we love from PMK. Actually, it's a whole lot of mad fun, but...that's just my take on it. Random historical notes!