My son has both (and had reflux) - but they are unrelated as far as I can tell, because when we eliminated dairy, he was became a much happier baby (less gas, less tummy upset, reflux was better although he still needed prevacid, etc). But he still got ear infections.
The only thing that cured the ear infections was tubes. They've been great.
I'm surprised the ped told you to take your son off of formula all together. There are several commercial formulas that do not have cow's milk in them. I use Nutramigen (by Enfamil) and Similac makes a similar one called Alimentum. You might try one of those.
Also, it is my understanding that many babies who are allergic to cow's milk are also allergic to goat's milk. I breastfed (used the formula for supplementing sometimes) and I could not eat feta cheese which is made from goat's milk because it made my son fussy, so I know that I certainly wouldn't have been able to give my son goat's milk instead of cow's milk.
All-in-all, if I were you, I'd have enough questions about this advice that I'd make another appointment with the pediatrician you know and trust, and discuss it further with him.