Depends on your tax situation.
With such limited info, it's hard to give detailed recommendations.
I'd probably roll it into Rollover IRA because I like having more control and that would remove a layer of fees, the 401k layer.
Plus if the market turns and the value drops below $5,000, the old employer might boot her anyway.
If you're in a low tax bracket, she could convert the Rollover IRA into a Roth IRA without paying any early withdrawal penalties, just paying income tax.
As previous poster mentioned, all IRAs are individual accounts as are 401ks. So all these account would be in her name.
By using "joint," did you mean that you contributed to it by using joint income or maybe based on your income, not her own?
HTH