Hi Vicki - St Margarets would have been a house, certainly not a church or anything like.
I've been up and down the census pages trying to place it in Lower Street. It would seem that the enumerater has it thus
1891 - Henley House,
St Margarets, Malthouse Buildings and The Red Lion. There are other houses between but they are not named.
1901 - Henleys,
St Margarets, Red Lion
Now - Henleys is still there a big house on the corner of what is now Rivermead.
St Margarets must be gone, probably on the site (or close to) of what is now Arundale School...a small private day school for girls and boys
Malthouse Buildings, was I beleive six houses - now the site of an assisted living type complex of flats been there since late 60's early 70's.
Red Lion - no longer a pub now a private house.....
If you go to Google Maps satellite view and bung in Pulborough, look for Lower Street, look for Rivermead. You will see that Rivermead is a road that goes off Lower St loops and comes back on to Lower St. D shaped on map.
Look along Lower Street between the Rivermead road...with Henleys in the left corner and the old Red Lion about two thirds the way along going, it would be East but right on the map...looks like this is an old view it's a grey plot with no trees, then St Margarets would have been along there somewhere.
Hope this makes some sense

Suey