The ruling of Halal (lawful) and Haram (unlawful) can’t be based on your thinking. If you are sure of the theft, you are not allowed to buy and sell it. Though you are personally not involved in any kinds of dealing, and you are the agent of the company, then also it is not right for you to proceed for the dealing. For, in the matter of business, the agent is responsible for all the dealings. And if there is no certainty, but only doubt, then it is allowable. And in this condition, though your salary can not be certainly ruled out as Haram but it is better for you to perform Hajj by borrowing money from any pious person and later pay the debt, so that you don’t have any doubt regarding Hajj in your heart.
Allah (Subhana Wa Ta’ala) knows Best
Darul Uloom Deoband