Granting of visa or rejection is not in your control neither you are responsible for it.
Instead of writing to the Poland Embassy alone,. you could have communicated this problem to your company too.
You keep them posted about the developments in this regard.
You cannot be held responsible for this debacle which is beyond your ability.
You can inform your company in writing about this visa problem and your inability to travel without visa being granted by Poland for no fault of yours,
You can politely inform your company that you canot be held liable for this payment as demanded by them for which you are not responsible hence you refuse the deny the payments demanded by them.
Legally this cannot be enforceable because the company has to arrange for yor visa since you are travelling on official duty and not a private visit.