This is an interesting question. I find nothing indicating Twain was anti-industrialist, though that isn't conclusive proof he didn't hint at anti-industrialism in his writings. Twain was, in, fact, extremely close friends with industrialist Henry Rogers who was instrumental in building Standard Oil into an industrial power. It is well recorded that Twain was certainly anti-imperialist being against the annexation of the Philippines, though there is no similarly strong record of anti-industrialism.
Supposing that Twain did intend Tom Sawyer to carry a subtle anti-industrialist message, he, as a skilled author, would put some hint of it in the exposition, specifically, in the first chapter of the story. If, on the other hand, an anti-industrialist message can be gleaned against Twain's will, as it were, through the application of Marxist literary criticism, hints establishing that thematic thread would very likely also appear in the exposition, specifically, in the first chapter.
As it happens, there are three early passages that may be looked at through the lens of Marxist theory as being subtly anti-industrialist. In the first, the new boy in town, with the "citified air about him" can be seen as the metaphoric representation of the industrialist powers of major urban centers. The fact the Tom Sawyer wins their tussle and makes the boy cry "Nuff!" would indicate the moral authority of working class and rural life over industrialism and urban life.
The more Tom stared at the splendid marvel, the higher he turned up his nose at his finery and the shabbier and shabbier his own outfit seemed to him to grow. Neither boy spoke. ...
"I can lick you!"
"I'd like to see you try it."
The boy only struggled to free himself. He was crying—mainly from rage.
"Holler 'nuff!"—and the pounding went on.
At last the stranger got out a smothered "'Nuff!" and Tom let him up and said:
"Now that'll learn you. Better look out who you're fooling with next time."
The second passage can be seen through Marxist theory to represent industrialist's manipulation of innocent and gullible--and powerless--workers into situations that are painted as opportunities but that are really prisons of exploited work, such as in steel mills and coal mines. Tom's voice would symbolize the manipulative voice of the industrialist in the famous Saturday fence white washing scene:
Yes, she's awful particular about this fence; it's got to be done very careful; I reckon there ain't one boy in a thousand, maybe two thousand, that can do it the way it's got to be done."
The third follows and shows the fat contentment of the industrialist who has just gorged himself on the exploitation of the weak-minded and needy worker. As the worker labors under adverse conditions on promises of livelihood that prove to be viciously inadequate, the industrialist sits with the rewards of his cunning. Tom represents the industrialist and the conned boys represent the exploited workers:
[Tom] sat on a barrel in the shade close by, dangled his legs, munched his apple, and planned the slaughter of more innocents.
Each of these early passages from Chapter 1 might be interpreted as subtle messages of anti-industrialism in Tom Sawyer. This thesis is certainly plausible as the age was one of growing industrialism and continuing disenfranchisement. [The format of answers on eNotes doesn't permit for examination of Huckleberry Finn.]