When you use the “Buy Stock” action it prompts you for the account to use. The accounts include your player account and any companies you control. I can’t test it to be sure (because my company has no shares outstanding), but you might try using “Buy Stock” to buy your own company stock with your company account. Even if the shares didn’t go away, they would still be functioning effectively as though they were gone.
Since you can’t just leave your bid out on the table, you might consider contacting individual investors to arrange the price to sell the stock back to the company.
-KnightAV