No, if you are filing separately, and have 1099's in both names, it is proper to each report half of the amount on your separate returns (or actually any split you both agree to).
Since on your MFS return, you give the SSN of your spouse, the IRS can see that the amounts reported on both returns add up to what is reported on the 1099.
If you're using TurboTax Desktop and care to use a 'What If' scenario to see what your returns look like MFJ vs. MFS, in FORMS mode, choose 'Open Form' and type in What-If.
@marinchip

**Say "Thanks" by clicking the thumb icon in a post
**Mark the post that answers your question by clicking on "Mark as Best Answer"