Your logic isn't flawed, but the differences in power requirements between a VW Rabbit and a Samurai are quite immense. They weigh a similar amount, but that's about it. The Samurai simply needs more power to move it down the road than the Rabbit. Since I grew up driving both vehicle types, (familiy has owned the Rabbit since '81 and the Samurai since '88), I think I can say that with some conviction.
For a cheap engine, pull a 1.3 8-valve from a Geo Metro Sedan/Suzuki Swift at the pull it yard. Same block/head as the Samurai engine and you can likely get them for around $100. Swap over the Samurai stuff on the outside of the engine and you have a cheap engine. Been there, done that.
If you want more power, pull a 1600 8-valve from Kick/Tracker, but you will also need an adapter kit but it's still a lot less than a diesel kit which starts at $400. The 1600 8-valve has considerable more torque (93 ft lbs) and hp (80) than the 1.6 NA VW Diesel. A much better engine choice for a vehicle that will see road use.
Everything I've ever been told or read about the VW diesels is that they were great offroad, but were downright horrible on the highway. The local guy with the 1.9 TD spent a lot of time, I would guess at least 50 hours doing the swap. If I recall correctly, he still had some cooling problems.
I'd hate to point you towards another board, but this BBS has a great diesel section:
http://bbs.zuwharrie.com/content?board=48.0After reading all the stuff on this board years ago, I wrote off the diesel as a viable option. Seem like it needs constant tinkering. I was really considering a diesel swap at one time (and I might eventually do it for the novelty aspect), but it seemed like the 1.3/1.6 Suzuki engine was a much better choice all around.
Anyways, if you keep the speed below 60mph, a Samurai will consistently get high 20s on 205/70 tires. Before the EPA ratings were recently revised, the Samurai had 28/29 city/hwy ratings which is actually pretty close to a stock Samurai mpg. The new EPA rating were supposed to take into account faster acceleration, higher highway speeds, a/c, ps etc, none of which really applies to a stock Samurai...which is still very slow and has no creature comforts.

Again, they didn't actually retest the Samurai, they just did some funky math to come up with the new number from the old.
As far as the stock rims, many people run relatively wide tires on the small rims because it makes it much less likely to blow a bead when you're offroading. You can really drop the air pressure in them. 235/75 isn't exactly pushing it on the stock rims either.