If I had a vehicle not equipped with A/C, I think the electric compressor might be a good option. Something to consider in all of this...if you adapt a factory setup, you are using a 40 year old compressor design. There have been advances in efficiency of all vehicle systems, including HVAC. If you are comparing apples to apples, then you would be using a belt driven compressor with modern design and comparing that to a modern electric compressor. The big question is whether or not the Suzuki compressor if variable output or not. They became common in the late 80s into the 90's. The improvements in efficiency would be much less or negligible compared to this style of compressor.
One thing that peaks my interest would be the ability to leave the AC running in my vehicle, without the engine running. Of course, you would need battery capacity for this, but I plan that for my rig anyways. Just imagine, turn off your engine, lock it up, and leave the ac blowing while you run into the store!
As far as the alternator situation...You already have an alternator operating in your vehicle, causing drag on the motor. By upgrading to a larger alternator, you are not starting from zero power drag. I would venture to say that there is a minimal difference in power drag for the stock alternator and an aftermarket high output unit. I have seen dyno testing on engines that have shown a 1 hp or less drag on an engine with a 100a or so alternator installed. I have been looking at electric power steering conversions for another project I am working on, but this gets me to wondering about just converting the PS to electric also. Massive electrical upgrades are on the list for my rig, so the charging system and batteries would already be in place to make these retrofits.
Another thing to consider is the availability of parts. I am not sure what parts you need to collect to mount the factory compressor set up on a Samurai, but the electric compressor would make that easier. Another concern I have personally is the ability to source a QUALITY replacement compressor for the failed unit currently on my Sidekick.
As is quite clear, there is so much to consider when making a modification liek this. Good luck with your research and decision! Keep us updated on what you decide to do!