Q:

What happens to Zadok Allen in The Shadow Over Innsmouth?

In Lovecrafts "The Shadow Over Innsmouth" the narrator talks to Zadok Allen, who tells him things he isn't supposed/allowed to tell.
This includes the following:

 "S'pose one night ye seed somethin' heavy heaved offen Obed's dory beyond the reef' and then learned next day a young feller was missin' from home. Hey! Did anybody ever see hide or hair o' Hiram Gilman agin? Did they? An' Nick Pierce, an' Luelly Waite, an' Adoniram Saouthwick, an' Henry Garrison. Hey? [...]"

The conversation ends like this:

 "Git aout o' here! Get aout o' here! They seen us—git aout fer your life! Dun't wait fer nothin'—they know naow—Run fer it—quick—aout o' this taown—"
 
 Another heavy wave dashed against the loosing masonry of the bygone wharf, and changed the mad ancient's whisper to another inhuman and blood-curdling scream. "E-yaahhhh! . . . Yheaaaaaa! . . ."
 
 Before I could recover my scattered wits he had relaxed his clutch on my shoulder and dashed wildly inland toward the street, reeling northward around the ruined warehouse wall.

 I glanced back at the sea, but there was nothing there. And when I reached Water Street and looked along it toward the north there was no remaining trace of Zadok Allen.

Zadok Allen isn't mentioned in the rest of the story.
Later, however, the narrator notices this:

 When the view of the water again opened out—this time on my right—I was half-determined not to look at it at all. I could not however, resist; but cast a sidelong glance as I carefully and imitatively shambled toward the protecting shadows ahead. There was no ship visible, as I had half-expected there would be. Instead, the first thing which caught my eye was a small rowboat pulling in toward the abandoned wharves and laden with some bulky, tarpaulin-covered object. Its rowers, though distantly and indistinctly seen, were of an especially repellent aspect.

Could this be Zadok Allen?

A:

I don't think so.  In your final quotation, the boat is "pulling in toward the wharves".  In the others, the objects were taken out to sea and dropped.
That's not to say that Zadok's final fate wasn't going to be what you're suggesting, though.
I remember the passage in your final quotation and always interpreted the object under the tarp to be

 a shoggoth, though now I doubt one would fit on 'a small rowboat'.

A:

Well, it is not explicit, but he is supposed to be captured by the people of Innsmouth and punished/killed. At least, in almost all the movie/game adaptions, that is what happens (the adaptions are more explicit, I guess :P).

