Sephiroth is fully aware that Jenova is not a Cetra and that she/it is not his biological mother.
He gained this information while aborbing the knowledge in the Lifestream.
As for Sephiroth wanting to fulfill Jenova's will, i don't think that's the case.
Apart from the fact that Sephiroth dominated Jenova's will and turned her/it in to his puppet, his plan in FFVII had nothing to do with what was seemingly Jenova's goals. He was fulfilling his own plans and pursuing his own objectives.
Sephiroth's goal in AC/ACC was more akin to what Jenova did centuries ago, but it seems that he decided to do such thing in his own will.
Why didn't he stop his plans after realizing that Jenova was not a Cetra and such?
Well, maybe because he didn't care anymore. Through Genesis' betrayal, Shinra's corruption, and with the secrets behind his own birth being the last drop, Sephiroth saw how rotten mankind had become and decided to
become a god and create his own paradise, regardless of what Jenova was.
Another point of interesting is that, through FFVII, Sephiroth's devotion to Jenova decreased a lot. In several scenes, Sephiroth referes to Jenova as "Jenova", not mother or anything like that.
Even in AC, in the japanese dub, while Kadaj and the others refer to Jenova as "kasa", wich means "mother" in a warm and dependable way, being more or less the equivalent to "mommy", when Sephiroth describes his plan, Sephiroth referes to Jenova as "haha", wich also means "mother", but in a more impersonal and objective way.
In my prespective, while Sephiroth still referes to Jenova as "mother", he sees her/it as nothing more than a tool, with his devotion to her/it completely gone.