The rare phrase backwards, the way Molly went to church means backwards, also reluctantly.
This phrase also occurs in the shortened forms the way Molly went to church and as Molly went to church.
This phrase is of unknown origin. It is allegedly a borrowing from Irish English (cf., below, quotation 3), but nothing seems to support this allegation; in particular, the phrase does not appear in any of the Irish newspaper archives that are available at present.
The only occurrences of the phrase backwards, the way Molly went to church, and of its shortened forms, that I have found are as follows, in chronological order:
1-: From The Commercial Bulletin (Boston, Massachusetts, USA) of Saturday 16th September 1865:
Business in New York.
FROM OUR OWN CORRESPONDENT.
New York, Sept. 15, 1865.
THE NAVAL TUG,
at the dock, between Paul Forbes’ Algonquin, and Secretary Welles’ Winooski, lasted 96 hours, and decided nothing. The vessels did not succeed in dragging the dock into the river. The public seemed to think that it was for this purpose they had been lashed to the pier. The race was to commence yesterday,—the vessels, according to popular representation, being bound to run “stern foremost,” as “Molly went to church.”
2-: From The Arena of Politics, published in the Sunday Morning Leader (Wilkes-Barre, Pennsylvania, USA) of Sunday 10th August 1890:
I’ve heard a man say whose authority is great on such matters, that more than twenty men have been promised the Wardenship, about twenty-five more night watchman at the jail and that the number for watchman at the “koort” house and mercantile appraiser would fill a small sized diary. They are all instructed to do what they can for the “boss” and if he is fortunate enough to be elected, he will see that they will all be taken care of. He will, the way Molly went to church.
3-: From ‘Scouse 1 Lingo’—How It All Began, by the Liverpudlian author and journalist Frank Shaw, published in the Liverpool Echo (Liverpool, Lancashire, England) of Friday 8th December 1950:
There are many Welsh and Scottish in the city but their influence has not equalled that of the Irish.
Perhaps we got from Wales kecks for trousers. Characteristically the Scot gave nothing.
Certainly from Ireland we received gob, gom, mam, the queer feller, webs, lug, moider, and phrases like Backwards the way Molly went to church and You’re strong as a bad egg.
Is it no wonder that, when Jim Phelan 2 came here, he thought (according to his autobiography “The Name’s Phelan”) he was in Dublin. Probably quite a few New York lads thought they were back in the Bowery 3.
Our early trade with America, in fact our trade generally all over the world, meant our returning sailor sons bringing fresh largesse to the Lancashire-cum-Irish mint.
1 The word Scouse refers to a person from, and to the dialect of, Liverpool, a city and seaport in north-western England.
2 James Leo Phelan (1895-1966) was an Irish writer, political activist and tramp.
3 The Bowery is a street and district in New York City, historically noted for its cheap hotels and bars frequented by the destitute and homeless.