3D is important for depth perception, eg. walking down stairs, gauging the speed of on-coming traffic when crossing roads or driving.
It's true that surgery is NOT a 100% 'cure' for strabismus, and like your doc says, if the muscle is overstretched in the surgery, the eye might move out in opposite direction instead.
At this point in time, you may want to get second opinion. Afterall, surgery is a major thing, especially at such a young age. Also, if your boy is already using both eyes, the surgery may be just cosmetic - to look nicer. This can be done when he's much older. As long as he's using both eyes he will have 3D vision.
Check with your doc again, what is the hurry, if your son is using both eyes. If the fear is that he'll develop lazy eye, ask what are the other options - patching, or surgery later, when it becomes obvious he's only using one eye.
Hope this helps. but remember, I'm not an eye doctor! You'll still need to check with the specialists. Just some questions for you to ask them.
All the best.