Probably a little sick and didn’t want to be stuck in Quito. Captain probably told him to stick around hotel until last minute.
A bit of Imodium, water, caffeine, and oxygen can do wonders.
I trust the Captain in these matters, I’m sure he was in the loop. Maybe the FO always looks rough and this was also a bad hair day.
What would I have done? Pretty much the same thing you did, I would have trusted the Captain.