I remember reading one where I think Dean gets migraines and they both end up at a teacher's house but haven't been able to find it yet,
found it!
Meddlesome Fools
https://www.fanfiction.net/s/4007668/1/Meddlesome-Fools
John drags his boys on another hunt, but unfortunately this time they weren't prepared. When a caring teacher discovers the boys' injuries, will her meddling help or hurt the family? A wee!chester story.


though I did find this link just in case you hadn't seen it -

http://spnstoryfinders.livejournal.com/9333718.html

and came across this one
Country of the Heart
http://archiveofourown.org/works/253327/chapters/393555
Written for spn_gen_bigbang. After being hospitalized for meningitis, fifteen-year-old Sam finds himself put in a foster home while John is investigated for suspected abuse. Against all of Sam's expectations, his foster family turns out to be a caring couple with the kind of home Sam only ever saw from the outside while he was growing up, making him feel even more conflicted about the kind of life his own family leads. To make matters worse, John leaves town to go on a routine hunt in spite of his upcoming custody hearing, prompting Sam to wonder if his own father and brother might be relieved to have him —and his constant demands for normalcy— out of the picture. When his father goes missing, followed by Dean when he goes after him, Sam quickly discovers that they need him just as much as he needs them, and sets out to bring his family back together again, for good.