My 15 yo son has cultured MRSA for about 8 years and his health has declined steadily since then. Our clinic had the "watch and wait" policy at that time and I cannot tell you how much guilt and regret I feel for not pushing much harder to have an eradication attempt made at that time.
This is compounded by having gone through a very similar experience when he first cultured pseudomonas and we were told that there was no eradication protocol. Now, of course, there is.
It seems, from my perspective, that there is very little downside to trying to hit it immediately and hard. If it doesn't work, well at least you tried and he's no worse off.
Best of luck to you!