Good information, Diane.
Others will have different takes on this but - all your speculations on Mary Ann/Marianne presently seem possible. Another possibility I suppose is that Mary Ann is William Henry's mother whom we only know as Anne du Bois.
Please correct me but my recollection is that our main source for any of this is a Burke's entry on the Halpins of Ford Lodge, Cavan (can someone please redirect me to a link for this?). And that information most likely came from someone in that family, open to the usual mistakes, misrecollections, guesses and lore that gather with time and sometimes outright self-serving fibs (not necessarily here).
However, I would think that the 1808 death would be that of Marianne Crosthwaite. Her son WH had not yet married.
The 1836 will of a Nicholas Halpin is very interesting if it is not Rev NJ Halpin, who died in 1850. Could it be that this is a will that NJ made in 1836, not one that was proved then? If it is not NJ, could it be a previously unknown brother of WH and uncle of NJ? There is every logic to that. Nicholas Halpin school owner of Portarlington would surely have named a son Nicholas if he had more sons than we know of. Is there a Nicholas Halpin about (other than Rev NJ) who would fit the bill. And, it provides another link to Meath (and Cavan?).
Bill