Hi
In the Greenwich area that early you are only going to have the original parish churches and not the daughter churches that were largely founded with a growing population in the C19th.
The London Metropolitan Archives guide (the link is given in the guide at the top of the London and Middlesex Rootschat boards to burials in the London area and given below) lists all the Anglican churches in the present day London borough of Greenwich and the date the registers survive from and whether the registers are deposited with the LMA or not and hence online with Ancestry.
http://c.mfcreative.com/offer/UK/Search/MoreHelp/London-Parishes-arranged-by-borough.pdfThe ancient parish churches listed are
St Alfege Greenwich (deposited with the LMA)
St John the Baptist Eltham (registers not deposited)
St Luke Charlton (deposited with Greenwich Heritage Centre)
St Mary Magdalene Woolwich (deposited with the LMA)
St Nicholas Deptford (deposited with the LMA)
This is the website for St John Eltham
http://www.elthamchurch.org.uk/Indexes and transcripts of the church registers are held at Greenwich Heritage Centre.
Where the LMA hold Bishops Transcripts - copies of the registers supposedly done once a year and sent to the Bishop (not always done, not always copied correctly and fully and not always surviving) these will be on Ancestry.
The Atkinsons may not of course have remained in the Greenwich area after the baptism of their children. Do their children marry in Greenwich?
Regards
Valda