Put another way, if you are married, typically your combined taxes paid will be the same whether you file Joint or Separate (ignoring things like the "no IRA deduction from MFS"), but the tax may be different compared to 2 unmarried people filing single.
Of course, I believe we found above that the bulk of the OP's problem wasn't as much the marriage penalty increasing total taxes as it was a somewhat inequitable split of the taxes between OP and OP's much-higher-income spouse in their split-finances arrangement.