You are correct that daycare expenses will not calculate, when you are file as married filing jointly and one spouse is incarcerated, unfortunately. To qualify for the credit, both spouses must work or one of the spouse must be a full time student or be completely unable of self-care... being incarcerated does not qualify as an exception to the above conditions.
If you file married filing separately, you are not allowed to take Dependent Care credit at all. Are you able to file as Head of Household (HOH)? You can qualify if the spouse hasn't lived with you for the last 6 months of the year, the child lived with you for more than half of 2016 and you paid more than half the cost of keeping up your home...If you qualify, file as HOH, you will be able to leave off your spouse's information off your return all together and qualify for the Dependent Care Credit.