Currently it is not possible to disable your signature for email templates sent via sequences, but since some users need multiple signatures a great addition would be to give the user the ability to supress his signatures for sequence emails.
That way he could simply supress his default signature and instead add the needed signature directly in the email template.
Currently this is possible, but only if you disable your signature in general, which on the other hand makes it more complecated to send regular 1-1 emails from contact records.