I don't know that there is a minimum time of noise exposure that will cause hearing loss, but I've always been told that loss is cumulative. I would think - - underline think, it's just my opinion - - that you can't be too careful, especially with young, developing bodies.
I wouldn't try anything that goes in the ear canal for a 3-mo-old. It might be painful or uncomfortable, and it might wind up in his mouth. But I'd definitely use one of those wool caps with the straps you tie under the chin so the little guy couldn't knock it off. Another possibility would be one of those straps that looks like a sweat band. Anything to cover the ears ought to help.
I'd be MORE concerned about discomfort during the descent. The largest pressure changes occur in the lower altitudes. Don't think that "only" 2000 feet makes it a non-issue. Make sure he has something to suck on during the descent.
.