It's been awhile since I've seen the movie but I came away with the thought that it was the guy who worked on the land/farm? But probably we aren't meant to know?

It seems to have been written so that what anyone personally concludes can be - and potentially is - correct. Norman Jewison stated, in his autobiography (quoted in this TCM.com article):

I think most people, regardless of their religion, regardless of logic, want to believe in something outside of their everyday lives. Outside of themselves....Agnes of God gave me the opportunity to explore that timeless human conflict between believing what we can see and believing what we can't see or experience. It seemed to me then, as it does now, that the world is in dire need of angels.

Considering the stigmata that Agnes experienced, I've always felt open to the possibility (though realize it may not have been what occurred) of immaculate conception in her case.

I believe Agnes would have remembered, while under hypnosis, and been tremendously traumatized, had the father been some man.