Vampires are not often left to fend for themselves, usually it is done when a vampire doesnt have permission from his/her clan to create them, or when the Prince hasnt authorised it, then again it does happen, and as long as they learn the proper order of things they would often be left alive, more often than not its happens to Caitifs aka thinbloods, they are a bad omen. Anyway obviously the MC is higher gen than that atleast 13th, but with his powers even 12th gen seems a little low, And since the Archon wanted to use him against Sharon, he had to have something that they thought was worthwhile to keep, and at that point the Archon couldn't just kill him, what use is a dead tool.
The MC's Sire mentioned rome from memory and how boring it had gotten over the time since then, she actually seemed older than rome from her attitude, so Id say yes, she was ancient, id guess she was of an offshoot from Toredor, there were several known branches, but I'd say she is a bit more separate than those known sub-clans.
Many in ancient times learned from other bloodlines, and if her blood was strong enough some of her powers would definately pass to the MC, she could even be powerful enough that while the archon and others probably have met her, she probably made them forget, why be bothered by youngsters like him afterall, he was a spoiled little brat afterall, the MC however had a fire that she liked.
If she was that old, some of that power could easily pass to the MC, infact it would be almost certain, so that the other vampires just treat him like any other 9th to 12th gen vampire, they wouldn't know to fear what he could become, and depending on how old she truely was he could even be 5th to 6th gen, the chances he would become a power to fear at that generation would be high, and that power would be unbelievable.
Heck, his visions give a hint that he is atleast 11th Gen as the only powers I remember like his from the books arent really accessible to lower generation vampires, and even at that level he could become a real powerhouse. Ammendment: I have found that some Caitifs, and thin-bloods can get a form of visions, I still dont think thats what we have with the MC though, Id stick with my belief that he is around 11th Gen, if only because of how well he can control what blood he had got. (Edit due to the book Time of Thin Blood, and the fact that if he was Caitif - Clanless, and a Thinblood they would have killed him for any breach of the rules)
She may well be seperate from the two main factions, someone messes with her they forget what they were doing, and either leave a "Dangerous Area" or she just kills them, the two men at that meeting were more than likely ancients, but they knew not to mess with "The Lady of the Temple". That sort of respect takes hundreds if not thousands of years for vampires to garner. And I know i've seen the term before, but Im not sure what book the temple was mention in, I think it was dark ages or similar, either that or it refers to her being the Keeper of the Elysium, which does seem to fit, may even explain why noone thought she might be the MC's Sire, the Keeper is too highly respected, and the Building being her Temple would also fit, vampires would know you dont mess around in her domain.
The worst crime is actually Diablerie, draining all of what a vampire is and gaining power from the act, destroying them in the process, although there are some cases where it has been allowed, and Tremere actually commited the act at the beginning of their clan.
Also people have mentioned the eastern vampires the Kuei-Jin, and some of their powers are truely scary if you could use them in the right way, some resisting to a degree the effects of sunlight, very few western vampires gain their secrets though, probably under a dozen total.
Generation is how far below the first vampire Cain you are, and 13th is the most distant they have allowed for, below that you are Caitif and usually too weak to worry about.
