jay, As for getting the bigger, badder, alternator, you can go into your local auto parts store and see what they can get for you. Besides, I just checked on e-bay and they have the 3G alternators for our trucks in the 250 amp setup for $170 delivered to your door.
As for an alternative to what you are doing, this is what I would say: install a battery on your trailer (deep cycle) and use the 7 pin harness to recharge the battery as you are driving down the road. The truck is already wired up to isolate any load in the trailer when you turn off the truck. No need for a battery isolator, no need for anything special other than adding a wire to the 7 pin connector on the trailer to go to the battery. Can't make it much easier. Then you can put a cigarette socket on the trailer for when you need power. Then, if you need to start your truck because the battery died, you simply unbolt the battery on the trailer (assuming it is still near full charge) and drop it into the truck to get you on your way.
I can not make it much cheaper than that. A battery isolator is THE!!!! way to go. The big thing that I will tell you is that you need to get a battery isolator rated for what your alternator can output. There are people that will tell you that you can use a solenoid to make things work. While what they say is true, it is also a double edge sword because something as simple as leaving the key on in the ignition can drain both batteries and now you are SOL.
If you need more info, let me know. I will assist however I can.