Re the CRF frames, they are mostly quite different. The CRF230 motor is based off the old XR200 motor though so you could swap for a kick-start only XR200 and save a fair bit of weight. Going with a smaller motor won't always help mpg. Motorcycle motors tend to suck a lot of fuel when run wide open and even the stock 230 is so gutless you'll have to absolutely flog it to keep up with traffic in most urban areas.
As far as mpg for the CBR250, 88 is extremely optimistic. Check out this month's MCN for real-world figures of the ninja 250, cbr and atk. Its a brand-new bike so no experience yet on how long it'll last, but I'd be extremely surprised if I ever see one worn out. Modern bikes, especially modern liquid cooled Japanese bikes are built really well and just don't wear out. They almost invariably end up sitting and rotting or getting crunched long before the engine gives up. I've seen a few honda sport bikes north of 200k miles that had not required any engine work.
Also with 250s you have to ride them really slowly to get great mpg. If you plan to have fun and keep up with traffic on the freeway you'll use just as much and sometimes more fuel as a big bike.
BTW I just got my wife a ducati monster 620. Its a cool little bike. Enough power for freeway work and general fun but very noob-friendly (she's not really a noob though) while retaining a boat load of character that you don't normally get with such accessible bikes. MCN's mpg figures for it are within a couple mpg's of their figures for the CBR250 and right at theirs for the ninja 250 and its a heck of a lot more fun. I'm sure if you rode slowly enough the 250s would do much better, but seriously, that'll never happen with me operating the throttle
Have fun!