Except the EIC isn't engaged in immoral/violent/underhanded practices? Mathilde is keeping a close eye on it and instilling best practices into it specifically to avoid that problem from manifesting. While the whole "Eastern Imperial Company" thing does harken to the East India Trade Company, it's simply a joke, not something to be taken seriously. The EITC was infamous for having its own (and massive) private army and navy, not to mention its own private (and large) empire, coupled with enormous abuses and atrocities. The EIC isn't even remotely interested in the same kinds of ambitions--it doesn't have its own private empire and doesn't want one; one of its core principles is "don't skin the sheep", meaning don't exploit your state or populations for the sake of profit, because you'll soon need that population and state to be as strong as possible so you don't die horribly to omnicidal monsters. The only private forces it has are ones strictly for protecting trade routes, and that actually is a vital service that benefits a lot more than just the EIC (since threats to trade routes are at best bandits, and at worst forces of Chaos).