Engels certainly opposed much about the way the business he worked for in Manchester was run – but he never had the control over policy that you suggest. The mill he worked at, Ermen & Engels, certainly was part-owned by his father – but it was run by the senior partner, Peter Ermen, who (not unreasonably) suspected that Engels had been sent in to monitor him, and so sidelined the younger man into decades of numbing clerical work.

I covered this part of Engels's life in an earlier essay which you can read in full here if it's of interest, but the relevant portions are these:

Engels had been sent to Manchester to take up a middle-management position in a mill, Ermen & Engels, that manufactured patent cotton thread. The work was tedious and clerical, and Engels soon realized that he was less than welcome in the company. The senior partner, Peter Ermen, viewed the young man as little more than his father’s spy and made it clear that he would not tolerate interference in the running of the factory. That Engels nonetheless devoted the best years of his life to what he grimly called “the bitch business,” grinding through reams of stultifying correspondence for the better part of 20 years, suggests not so much obedience to his father’s wishes as a pressing need to earn a living. As part-owner of the mill, he eventually received a 7.5 percent share in Ermen & Engels’ rising profits, earning £263 in 1855 and as much as £1,080 in 1859—the latter a sum worth around $168,000 today.

What made Engels different from the mill owners with whom he mixed was how he spent his wealth (and the contents of Peter Ermen’s petty-cash box, which was regularly pilfered). Much of the money, and almost all of Engels’ spare time, was devoted to radical activities. The young German fought briefly in the revolutions of 1848-9, and for decades pursued an intensive program of reading, writing and research that resulted in a breakdown as early as 1857 but eventually yielded a dozen major works. He also offered financial support to a number of less-well-off revolutionaries—the most important was Karl Marx, whom he had met while traveling to Manchester in 1842. Even before he became relatively wealthy, Engels frequently sent Marx as much as £50 a year—equivalent to around $7,500 now, and about a third of the annual allowance he received from his parents.

Engels's disgust at the products of the system he was part of were real enough, however:

His acquaintance with Manchester’s worst slums is a matter of some significance. Though he had been born in a business district in the Ruhr, and though (as his biographer Gustav Meyer puts it) he “knew from childhood the real nature of the factory system”—Engels was still shocked at the filth and overcrowding he found in Manchester. “I had never seen so ill-built a city,” he observed. Disease, poverty, inequality of wealth, an absence of education and hope all combined to render life in the city all but insupportable for many. As for the factory owners, Engels wrote, “I have never seen a class so demoralized, so incurably debased by selfishness, so corroded within, so incapable of progress.” Once, Engels wrote, he went into the city with such a man “and spoke to him of the bad, unwholesome method of building, the frightful condition of the working people’s quarters.” The man heard him out quietly “and said at the corner where we parted: ‘And yet there is a great deal of money to be made here: good morning, sir.'”