Well, I've considered this, and you might be able to just lace them evenly, put the freewheel tool in a vice and turn the rim anti-clockwise. The rim should turn until the spokes pull tight, at which point you just have to break the freewheel loose as if the wheel were fully laced. Evenly is the important bit - if a spoke is missing, you'd have to miss a hole too.

I've never tried this, so I'll leave it to others to find any flaws with it.