Hmm I see the problem.
According to my Gazetteer, Holywell Lane did fall within the parish of St Leonard, Shoreditch High Street.
A local map here confirms this:
http://archivemaps.com/mapco/parish/parish10b.htmHomerton is a bit further North-East - several parishes away in fact.
As Nanny Jane says, it might a case of your ancestor not being entirely clear about her own birth place.
If the baptism date, names and occupations fit I would be inclined to accept this as "just one of those things".
If not, I think you would need to check the records for St John-at-Hackney which was subdivided , spawning the parish of Homerton in 1846.
http://en.wikipedia.org/wiki/Hackney_%28parish%29The records for St John-at-Hackney are, I believe, held at the London Metropolitan Archive.