Strange. I can't think of any other reason that you wouldn't be able to pay using direct debit. Here's a TurboTax FAQ about direct debit.
What is direct debit and how does it work?
Are you just not seeing that option at all? Are you being given ONLY the option to pay by check? You know you can also use Direct Pay offered on the IRS website (rather than writing a check). Here's a link to the payment options via the IRS website:
Payments | Internal Revenue Service (irs.gov)
I'd like to investigate this a little more. Are you using TurboTax Online (web-based) or Desktop (CD/Download)?
*** I am NOT a tax expert. I am a seasoned TurboTax user, and volunteer to provide assistance to TT users. Nothing I post is to be considered TAX ADVICE; I bear no legal liability for responses.***
