No, the IRS will not take your refund if you file as Married Filing Separately.
However, it might be more advantageous for you to file jointly, and include an Injured Spouse allocation. That way, they will determine which income belongs to who, and only take what she owes from her portion of your joint Refund.
Though an Injured Spouse return takes longer to process, it might be worth it if it significantly increases your Refund. Try it both ways in TurboTax to see.
Here's How to File Form 8379, Injured Spouse Allocation.
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