You didn't mention miles. If this is a low mileage vehicle you intend on keeping a long time, I wouldn't really flinch at $1k for rust repair, if it was a true repair (cutting out the bad metal, coating the backside / welds, paint matching the front side, etc. I like keeping my vehicles clean and that's actually pretty cheap. My mom has a 98 or 99 CRV and spent a couple grand having the quarter panel repaired or replaced because of rust underneath the gas filler area. But she keeps vehicles a LONG time and the rest of it looks great so it made sense to her.
But financially I can't think of a scenario where it really makes sense unless it was an ultra low mileage vehicle you were going to sell for top dollar. But if that was the case I'd just keep it still because it should be good for 200k+ miles.
Another thing, even though Hondas are known for rusting at the back of the wheelwells (CRV, Accord, Civic, etc., they never figured out how to do it right), they generally are solid underneath. But it wouldn't hurt to check as someone else said. Strut towers, subframes, etc., can get dangerous if in an area where salt is used. There was just a recall issued for 01-06 (I think) Escapes for rusty subframes and control arm mounts snapping off. That will get you upside down, in a ditch, on fire pretty quick.