No, if you have Family HDHP coverage, then the Family limit of $8,550 is shared between the spouses. TurboTax will share the limit automatically so as to minimize the excess or to reduce it to zero if possible. Thus for you to contribute as if you were under Family coverage at the same time that your spouse was contributing as if under Self coverage will trigger excess contributions. If your spouse if using Self-only coverage limits for certain months, then you cannot use more than the same Self coverage limit (not full Family) for the same months.
I imagine that things will go worse for you if you file separately, if for no other reason than the difficulty of entering things the way you want under MFS.
You generally want to withdraw the excess if you can. The reason is because any excess not withdrawn by the original due date of the return is carried over to the next year to be used as a "personal" (line 2 (8889) contribution) and is charged a 6% penalty.
If you are a disciplined taxpayer and are sure to reduce your HSA contributions for the next year AND are sure that you will have HDHP coverage the next year, then you can "let the carryover ride" at a 6% cost, and use up the carryover in the subsequent years. You need to count on your fingers to see which is better for your situation...as I said, withdrawing is generally preferable, if you can do it.
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