Can the penalty for not taking the total RMD be waived?

Yes, the IRS may waive the penalty if the owner establishes that the withdrawal shortfall was the result of reasonable error and that they will take reasonable steps to remedy the shortfall. To qualify for this penalty relief, you must file IRS Form 5329 and attach a statement of explanation to the tax return.

See the instructions for Form 5329. Your CPA should be able to give you guidance on this.