Though I'm generally of the view that arguing over details of the plot is not a particularly interesting way of reacting to a book,* and better analyses involve considerations of structure, pacing, voice, composition, etc, here we go:
I don't see how anyone could possibly root for Rochester.
The absolute worst thing one could say about St. John would be to make him equal to Rochester in ill-treatment of Jane. Both are attempting to use her for their own ends, and want to cultivate her responses to them without informing her about what is going on. St. John, however, reveals his motivations much faster, of his own volition, and at least has them aimed toward a noble purpose. As Jane herself admits, but for his insisting on marriage without love, there's nothing wrong with his plan. (A significant 'but,' of course, though it seems less a fault of an unforgiving nature than a crucial mistake made by someone focused on his vocation/too young to think through all the consequences involved.) Rochester, by contrast, holds his peace until he is forced to reveal all, and would implicate Jane in a crime without her knowledge or consent--I presume his requirement that she wait a year and a day after the wedding to ask about the other woman in the house to be one that would make annulment impossible. He is, in other words, willing to run her great legal and social risks without informing her. That's not to say St. John is better--I think the obvious best outcome for Jane is to live at Moor House with Diana, and never marry.**
The novel itself is lively and modern, and the direct narration a good deal more sophisticated than, say, David Copperfield. It's rather, in its own way, a good commentary on the action delivered by one of its players, not unlike All About Eve. That it unfolds as a combination of the most unlikely happenstance is not a matter of great concern to me as a reader--Jane is discovered in the end by the family she did not know herself to have, but the knowledge is not at all essential to the action as it is happening.
*Not interesting because it involves arguing over a stipulated and limited set of facts (the text), which then involves one in the equally difficult games of guessing the author's intention (as something distinct from the actual words the author chose to write, and retained after editing; for which there might be supplementary evidence in notes and letters, but for which none often exists) or reading facts and relationships not written into those stipulated, an endless game. It is also almost always an exercise in wish fulfillment or enforcement of orthodoxy--making the novel into The Thing The Reader Wants It To Be, which is flattering to their own beliefs and prejudices, rather than The Thing That It Is.
**And, yes, I get that the point of the novel is that circumstances come about wherein Jane can freely choose Rochester, and we are meant to acknowledge it as a free and unforced choice, and that is a good thing. But we've also probably all had the experience of dealing with friends who make free and unforced decisions that are nevertheless poor.