I had thought of making a shim with a cut out to miss the extractor but it seems a mickey mouse/bubba solution. If the barrel timed/clocked  correctly on other receivers it would seem the receiver is slightly off. Could be wear caused by the loose barrel or just slightly off when made.
The only Krag barrel I removed was not excessively tight, the tools I used are pictured in the sporterizing howto thread. I have seen pictures of guys really straining with 4 foot cheaters to get barrels off, I do not think many Krags are that tight. So you could probably use the tools on hand.
If the barrel is extra good and you do not mind using aftermarket sights and can enlarge the extractor cut, tightening it to a moderate torque maybe 40 to 80 foot pounds could work.
Others with more experience or welcome to chime in as I am only an expert on the one I have done.
As a trial to see if this idea has any merit go ahead and tighten it up and see how far off the marks it is. Guesstimate 40 lbs on a foot long wrench. Check the head space while you are at it.
Maybe this barrel belongs on another receiver and you get one made a little extra long for this one?