Keep a copy of the form and you don't have to check the box. You can write on the form that the employer refused to sign the T2200S and that you are filing the claim for the deduction because you believe you are eligible under the income tax act.
If it went to appeal or tax court you wouldn't be lying because you didn't verify that the employer signed the form. Remember it's not the form itself but the tax act that determines eligibility for deductions. The T2200S is just an easy way to prove that you were required to work at home by the employer. Most employers will sign it so for CRA it's a quick and easy way to determine your status. You can prove it in other ways though.
