IRC §1362(d)(1) indicates that revocation of the S corporation election such that the company would never be treated as an S corporation would have to have been made by the 15th day of the third month of the S corporation's tax year, otherwise the revocation will be effective at the beginning of the following tax year. Since you have missed deadlines for filing Forms 941, you are apparently beyond the 15th day of the third month of the S corporation's tax year, so the company must remain an S corporation for the current tax year.
You might be eligible for first-time penalty abatement:
https://www.irs.gov/businesses/small-businesses-self-employed/penalty-relief-due-to-first-time-penal...
