Just to give you an update, as it turned out I didn't manage to wait that long to take me long to decide I could justify ordering another marriage certificate(

) and it came today. Details as follows:
Jonathan Wilkinson & Elizabeth Alderson married on 9th feb 1852, in St Giles, Durham.
Jonathan is a minor, Elizabeth is of full age.
Both are in residence at Dragon Villa.
Jonathan's father is named as Matthew Wilkinson (Waggon-man).
Elizabeth's father is named as Thomas Alderson (Farmer).
Witnesses to to the marriage are William Tilly and Jonathan Wilkinson (his mark).
So there is more evidence to support this christening:
2 possible baptisms, 1st looks likely, 2nd is probably for the one Jen found in 1841:
Houghton-le-Spring St. Michael & All Angels
29 Nov 1833 Jonathan Wilkinson, of Middle Rainton, born 9 Oct 1833, son of Matthew Wilkinson & Mary
I also think that the Jonathan Wilkinson who is a witness to the marriage fits in well with the 1851 census return I found with a younger Jonathan listed as a nephew.
Another potential record that was brought up as a possible for Margaret, that jumps out a bit more (if she is Jonathan's sibling is this one):
Pittington St. Lawrence
22 July 1838 Margaret Wilkinson, of Pittington, child of Matthew Wilkinson (waggonman) & Mary
It also puts Elizabeth's latest dob at 1831 (contrary to nearly all later census returns). I'm not sure how many years she might have knocked off, but there is a baptism record for an Elizabeth Alderson born to
Thomas and
Margery (possibly connecting nicely back to the lodger with the Wilkinson's in 1851), Barnard Castle, 1829, which seems a stronger possibility now.
Would be grateful for anymore help finding Matthew in 1841 (I think I am happy to take him as found in 1851 with the witness link) and Elizabeth in either 1841 or 1851 based on this new information.
Thanks