Yes, Lemuel Covell the Baptist missionary was in fact the son of Phebe Paine.
There is a rather rare book, published in the 1830's.In the book, it is clear that Lemuel's mother's name was Paine, and that she was killed by her third husband, and that his father died when he was very young.It also gives accounts of his missionary journeys.I was able to obtain a copy of the book, but no copies are currently available for sale world-wide.
My interest in Lemuel Covell is that he was a personal friend of my 4th great grandfather Deacon John Rouse of Pittstown.John Rouse was the treasurer of the Missionary Society, and held the money for the missionaries.According to the book, after Lemuel's mother was murdered, John went on a trip with Lemuel to the places he lived growing up, to help ease Lemuel out of a deep depression.And, after Lemuel died out on the frontier, it was John Rouse who was called on to break the news to his family that Lemuel had died.
The name of the book is Memoir of the late Rev Lemuel Covell, by Mrs DC Brown, Lemuel's oldest daughter, and is published in the same cover with the memoir of Alanson Covell, his son.
This message is perhaps a little late, but I haven't been checking the Covell boards lately.