One thing to consider now that todays fuels almost always contain at least some percentage of alcohol. The alcohol will absorb a small amount of water and allow it to disolve into the fuel. This prevents the water accumulation at the lower reaches of the tank you might otherwise see.
So I agree, if the tank is essentially just flash rusted, a mechanical means of cleaning (bbs, nuts, rocks, etc) will be fine, just make sure to coat it with some oil immediately afterwards to prevent further flash rusting. From everything I've seen over the years, liners should more or less be a last resort for a pinhole leak. Just seem like way too much trouble for the minimal protection they afford. My opinion of course.