I suppose so, but I've never seen IRS send a check back, and if the taxpayer doesn't know how to use EFTPS it's probably easier to pay the 2% fee or ignore the bill.  Not that we would advise them to do that. 

"We may charge penalties if you do not make required deposits on time, make deposits for less than the required amount or if you do not use EFTPS when required. We will not charge penalties if you did not willfully neglect to make a proper and timely deposit and you have a reasonable cause."