I was unaware of this, not having read Paine's biography, but related in 
Scharnhorst's "Early Years":

/He had been ill with cholera at Damascus, a light attack; but any 
attack of that dread disease is serious enough. He tells of this in the 
book, but he does not mention, either in the book or in his notes, the 
attack which Dan Slote had some days later. It remained for William F. 
Church, of the party, to relate that incident, for it was the kind of 
thing that Mark Twain was not likely to record, or even to remember. 
Doctor Church was a deacon with orthodox views and did not approve of 
Mark Twain; he thought him sinful, irreverent, profane.//
//
//"He was the worst man I ever knew," Church said; then he added, "And 
the best."//
//
//What happened was this: At the end of a terrible day of heat, when the 
party had camped on the edge of a squalid Syrian village, Dan was taken 
suddenly ill. It was cholera, beyond doubt. Dan could not go on—he might 
never go on. The chances were that way. It was a serious matter all 
around. To wait with Dan meant to upset their travel schedule—it might 
mean to miss the ship. Consultation was held and a resolution passed 
(the pilgrims were always passing resolutions) to provide for Dan as 
well as possible, and leave him behind. Clemens, who had remained with 
Dan, suddenly appeared and said://
//
//"Gentlemen, I understand that you are going to leave Dan Slote here 
alone. I'll be d–d if I do!"//
//
//And he didn't. He stayed there and brought Dan into Jerusalem, a few 
days late, but convalescent./

As this is not mentioned in Innocents Abroad, the chronology of the Long 
Trip must be a bit inaccurate.  I'm wondering where and when this 
actually occurred and when did Sam and Dan actually get to Jerusalem.

-- 
/Unaffiliated Geographer and Twain aficionado/