I think it very unlikely that Sephiroth is a puppet of Jenova. Exhibit 1, the largest of Jenova cell-cultures is in Shinra building, yet Jenova breaks out, takes on Sephiroth's form and travels to where he is, in North Crater, which strongly suggests Sephiroth is exerting his will on Jenova, not the other way around.
Jenova has no reason what so ever to favor Sephiroth, or go to special lengths to facilitate what is ultimately in his best interest, not hers.
This is brought to crystal clear light with exhibit 2 - the fact that you kill Jenova prior to killing Sephiroth, whom is essentially acting as a shield trying to stop Cloud and Co from reaching Sephiroth, and when she dies nothing changes what so ever as far as Sephiroth is concerned. If fact, he doesn't even seem to notice or care.
Finally, although this is part speculation.
Fact : Jenova was based off of Carpenter's "The Thing", and the FFVII's concept stage of productions tied together with Parasite Eve, which features organisms that fit the theme of "The Thing" and are similar to Jenova.
Speculation : Jenova is not sentient. In fact, Jenova is kinda like a virus, the form of which we see in the game is probably just the last human/ancient host of it.
Jenova cells exert some kind of influence on an instinctual level through biological alteration, but Sephiroth having been born with it, and then falling through the life-stream absorbing the knowledge and power of the Ancients puts the virus in check, and uses it to further his own agenda, an agenda that is party influenced by the change in his nature as a result of having been born with Jenova cells to begin with.
Jenova being in control of Sephiroth just doesn't compute with what the game tells us explicitly though, just saying it makes even less sense thematically with what is arguably being implicitly stated too.