Like anything else, it really comes down to time, money and common sense. Having just rebuilt my t-case and transmission and a full frame off resto within the last 4 years, let me present some numbers to you.
T-case rebuild (I was lucky and only had to have a rebuild kit and no gears)
Anywhere from $75-200 depending on supplier and kit
Tranny rebuild (Rebuild kit, OEM 1st gear, 2nd gear, main shaft, input shaft, sealed front bearing)
$600 (I'm including shipping and estimating low in case my wife ever reads this post.....)
Oil, sealants and misc supplies
$100
Already we are up to approximately $850 for just the t-case and transmission. If you start looking at having to rebuild the front and rear differentials and steering, I would bet you can add another $800-1000 pretty quickly. This is just the parts bill and performing the labor yourself. Count on the jeep being down for around a month while you wait on parts and complete the rebuild.
Right now on Craigslist in my local area, you can buy a brand new car hauler (tandem axle 7K GVW) for $1650. A used one can be found for around $900. You drive the jeep on the trailer, strap it down, tie the windshield down and take off. Total time is about 15 minutes. No disconnecting drive shafts, no bungee straps on the steering wheel, no worries about backing up and you can drive on the interstate at 70mph safely.
CAN a Willys be flat towed? Maybe........maybe not.
SHOULD a Willy's be flat towed? Probably not.
As an added bonus, you now have a flatbed trailer to go pick up another jeep

Good luck!