Basically the radio system you received is specifically equipped for high performance electric park flyer aircraft and/or microhelicopters instead of regular sized glow planes. It sounds like you've actually received the right radio transmitter:
http://www.futabarc.com/radios/futk54.html
The 6EXA Super is available in either FM or PCM versions, which merely identify the included flight pack.
Any version of the 6EXA Super can be switched between FM/PPM mode and PCM mode. It sounds like the hobby store might have sent the more expensive FUTK53** model to fill your wife's order. If this is the case, they didn't do you a disservice. You received a PCM receiver worth about $80 instead of the standard $60 receiver.
The transmitter is the same as all of the other 6EXA Super packages. What you didn't get are 4 S3004 servos, power switch, and a receiver battery. You can keep the radio package they sent you and buy the rest of the components you'll need seperately. The PCM receiver you received will work in a Kadet LT-40, and you could use one of the micro servos for the throttle control. You'd just need a battery, power switch, and 3 standard servos to finish your plane.
If the place your wife ordered the radio from is now out of business, I believe I would simply keep what I had rather than risk returning the merchandise to a now defunct reseller. The 3 servos, power switch, and receiver battery are another $50 or so worth of expense, but the radio and receiver that you have will get the job done.
Edit: After re-reading your initial post, I now realize that you weren't saying that the hobby store is out of business. Basically, you simply need to ask them to exchange your FUTK53** for an FUTK56**, which is the radio system that comes with a standard FM receiver, receiver battery, switch, and 4 standard servos.
If, when asked what the radio would be used for, your wife told the hobby store that it was for a "basic beginner's plane" or an "entry level trainer" then the clerk who helped her probably thought he sold her the right radio.
I don't think that the hobby store was trying to get one over on you, they just didn't have enough information.
Good luck!