It will, but not an unsurmountable one.
There are two ways to do a QDRO. By amount and by percentage.
My guess is that your spouse will want to determine the value of the account before the loan and divide that value in two.
Example: $100,000 in account before the loan, $20,000 loan leaves $80,000. She gets $40,000 for her account, you get $40,000 for your account and still have to pay off the loan.
When served with a QDRO the custodian of the 401(k) will divide the accounts into two accounts, your original account and a separate 401(k) account in your spouse's name which she can then roll over into her own IRA.
Understand that a QDRO is a court order so you have to be very specific in how you want it handled.