I found a nut and washer that would give me a good amount of spacing, bearing will be about 1/32 proud. nut was put up against the cone to serve as the cone's lock nut and the washer was put on after
Bearings were re-greased and everything assembled. Another nut was put on the freewheel side to hold the new bearing in and to clearance between the freewheel and the frame
I've ridden the bike several times now with a bunch of stand-still to full throttle starts. I haven't taken the axle back out to check for sure, but it looks like it's still straight. I hope this can help someone else with axle bending issues.