I'm pretty sure doctors in general are not opposed to the use of earplugs. Doctors don't want you putting things like Q-Tips into your ears, because it's really easy to irritate the ear canal or worse accidentally puncture your ear drum. Ear plugs don't carry much risk (no chance of hitting the ear drum unless you're shoving them in with a stick, and should be gentle enough on the ear canal), and they are a very good idea if you're going to be exposed to loud noises. Good ear plugs can block as much noise as good earmuffs.
Doctors themselves (or their technicians) will put earplugs into your ears if they need to block noise, e.g., for an MRI or a hearing test.
I would warn not to use them all the time. Let those ears breath. I only use them when I need to focus very hard or when it's very noisy.
http://www.amazon.com/Protection-Professional-Folding-Padded...
Judging by how it seems to be the most used in industrial applications.
I use earplugs with over the ears headphones.
You could instead use over the ears noise protection with little in-ear headphones inside.
The only reason I don't do that is that my headphones are worth $1000+ and I wouldn't want to trade them for earbuds. Otherwise, your idea could very well be superior to mine!