Hope your having an awesome time in south america regardless. I'v got a physio buddy trekking around there right now - it's a shame he's going back to manchester in a few days cause I think he's not far from santiago.
Anyway - MCL strains shouldn't hurt in sitting... the ligament isn't under load so it should be feeling good. it may hurt because it's inflammed from chronic loading due to your overpronated feet - you never got orthotics to help with that did you? that may have been what it needed to prevent you from stressing the ligament while playing sport... I'm wondering wether you perhaps have a meniscal injury because of your knees ability to be fine with walking long distances and then worse after being in sustained flexion. - these usually will appear on Wikipedia reference-linkMRI, though if it's quite minor then maybe not. Electrotherapies won't do much for it - avoid physios who will use that as their primary treatment. It's quite possible that both the Wikipedia reference-linkmeniscus and MCL are damanged.
I'd suggest taking it easy and waiting till you can see a good physio? maybe get someone to tape your arch of your foot to help with the pronation to help reduce the stress going through it. You are unlikely to hurt yourself more unless you have a traumatic injury or go for some massive hikes without good shoes to support the arch.
Good luck - hopefully someone else will have some other ideas also