Addressing the more general case, it's important to note that possessive pronouns don't necessarily imply ownership, possession (nor does the Saxon genitive 's, despite what it says in that link).
Often, it just implies is some kind of relationship, connection. For reasons that aren't clear to me, teaching materials for non-native speakers frequently over-emphasize the "ownership" relationship (and make too much of the fact that we're slightly less likely to use 's after "inanimate" nouns - despite clear evidence that the car's engine, for example, is far more common than the engine of the car).
Regarding OP's specific context, I'd say it's a "non-problem". Native speakers don't simply assume My company went bankrupt implies the speaker owned the company, unless context favours that interpretation (as opposed to it just being the company the speaker used to work for).
But in the unlikely event that both interpretations are possible in a "non-interactive" (written) context, a considerate writer could easily disambiguate by using the company that I owned / that I worked for.