Which is not to excuse any of this, but please get the timeline right. :)
It was only going into the 19th century that anything resembling control or oversight started to come into being. Which in no small part led to their disestablishment.
Edit: if I built a fleet of warships, flying the US flag, escorted by full US Navy warships began starting shooting wars with other countries, can the US government just go "not us, private citizens, we don't have anything to do with that"?
The company was far more a relic of the earlier age - when the sovereign gave favour, handed letters of marque and established privateers. The East India Company and the Dutch East India Company similarly were more corporate states than companies as we might recognise them.
The history is incredibly complex, worthy of many books, but for the period of roughly 1600-1800 the EIC was closer to the independent Nassau privateers turned pirate than to a regulated, and at least somewhat controlled, London plc. At some point early in their existence they remodelled themselves on the VOC (Dutch EIC) model to become more state-like as the VOC was so successful. The VOC was more independent nation state until the very late 18th century too.
They both fielded armies and navies independently and distinct from Britain or the Netherlands, made and enforced treaties in their own, not national, interests, had their own systems of justice etc. Being amongst the very first stock based institutions there were no systems of oversight and control. Stocks were still traded in coffee and tea shops, despite the recently established Royal Exchange - where stockbrokers weren't allowed. It was one of those coffee shops that would eventually became the London Stock Exchange. Any regulation came much later, and slowly, and ultimately led to the disestablishment of the EIC, and the wide range of corporate and stock law.
I might also blame government for not seeking to constrain the company earlier than they did... I can't really blame them for not regulating something that was new and unknown, just as in the current era bitcoin has seen regulation start to come long after its success. Or the talk of regulating Facebook, or no end of others...