It was because he had such need of her.
I don't know whether you remember, but there were once some children who played at Jacobites in the Thrums Den under Tommy's leadership.
Elspeth, of course, was one of them, and there were Corp Shiach, and Gavinia, and lastly, there was Grizel.

Had Tommy's parents been alive she would not have been allowed to join, for she was a painted lady's child; but Tommy insisted on having her, and Grizel thought it was just sweet of him.

He also chatted with her in public places, as if she were a respectable character; and oh, how she longed to be respectable! but, on the other hand, he was the first to point out how superbly he was behaving, and his ways were masterful, so the independent girl would not be captain's wife; if he said she was captain's wife he had to apologize, and if he merely looked it he had to apologize just the same.
One night the Painted Lady died in the Den, and then it would have gone hard with the lonely girl had not Dr.McQueen made her his little housekeeper, not out of pity, he vowed (she was so anxious to be told that), but because he was an old bachelor sorely in need of someone to take care of him.

And how she took care of him! But though she was so happy now, she knew that she must be very careful, for there was something in her blood that might waken and prevent her being a good woman.

She thought it would be sweet to be good.
She told all this to Tommy, and he was profoundly interested, and consulted a wise man, whose advice was that when she grew up she should be wary of any man whom she liked and mistrusted in one breath.
Meaning to do her a service, Tommy communicated this to her; and then, what do you think?
Grizel would have no more dealings with him! By and by the gods, in a sportive mood, sent him to labour on a farm, whence, as we have seen, he found a way to London, and while he was growing into a man Grizel became a woman.