For MFS, they either both itemize or they both use the standard deduction.
When you run the MFS calculations, from what you described with the husband paying the mortgage from an account solely in his name, he would get the entire interest deduction, and she would have to itemize even though the standard is higher.
If you are still using Drake, in order for it to properly analyze joint vs separate returns, I believe you must have three separate input screens (and please make sure that the program doesn't show one itemizing and the other using the standard):
one for the mortgage interest and any other potential deductions paid solely by the husband with "T" indicated at the top
one for any potential itemized deductions paid solely by the spouse with "S"
and a third one for any potential itemized deductions paid jointly with "J"
Please watch for the state impact as well when presenting them with which filing status provides the best overall choice.