The thumb throttle used to bother me more than the finger did, but I've been riding for quite a few years now and I experience zero fatigue even after 3-4 hours now, I guess I'm used to it.
Both of my ski's now have the finger, and I do tend to "cruise" on flat water with 2 fingers and "hop" in chop or rough water with only one finger to have a better grip on the handlebars, and that helps somewhat.
If your fairly new to the sport I might say your hand will get stronger over time.
If your not new, then i'm guessing maybe that your spending a lot of your time with a heavy throttle, jamming to high rpm's maybe a little to much, or too often ?
I've learned over time to relax both hands quite a bit when its not necessary to have a hard grip, ie: cruising.. And that does help as well, occasionally I catch myself gripping too strong when its not necessary and have to force myself to relax and let the ski do the work, most of the time I'm just guiding the ski along the path.
I'm not saying that you need to drive in a straight line more, but maybe that you can just relax your grip a bit more frequently when not heading into a hard turn.
Not sure if that helps.