Good question, I can't claim to have a clear opinion on the subject. Thinking about it too much causes me to question the nature of fanon.

One thing I like about TF2 is that it's so easy for fans to interpret and work with the characters, and it hardly ever seems wrong just because it's not canon. I'm not usually big on OCs, however. This may just be because I often lose interest when I no longer recognize them as the characters from the game. I guess I'm fine with any interpretation as long as it retains the traits I like in that character. It's not up to me to decide if it's a valid interpretation, though. Obviously some writing looks more like canon, but it's not technically canon either way, right?
I think canon itself is pretty subjective stuff and not always clear-cut, especially with a piece of fiction as dynamic as TF2.

I see canon vs. non-canon as more of a continuum...

1. Is the character backstory consistent with the Word of Valve? The Meet the Team videos, the trading card information, the wiki, the in game voice commands, the comics, the blogs, etc. All else aside, that's what I take to be "factually" true about the cast, unless Valve says "nope, that wasn't canon" (like in the case of the Mac comic). Where Valve is more vague (like whether the BLU Spy is schtupping the RED Scout's mother or not), I assume so because of the voice commands, but I still label it as "personal headcanon sort-of supported by canon material, but I wouldn't cry about it if Valve came out and nixed it".
2. Is the character consistent with in-game (non-griefer) behavior and habits? This was the source I relied to for characterization before some of the later Meet the [Team] videos came out. So in my mind, Sniper and Engineer were pals long before it was suggested in the promotional videos because as an Engineer, I would tend to plunk dispensers next to Snipers. Medics were super-stressed and grumpy all the time, and hated Heavies who acted like Medics were their personal pets and acted ridiculously reckless while being healed, because that was how I acted as a Medic. And so on and so forth. This one, I tend to defer to canon wherever contradictions appeared, but I still prefer my version. So I don't mind stories where the members of the team actively hate each other and can barely work as a cohesive unit because I've been on those teams, but I don't consider those stories of THE cream of the crop RED team because that nonsense would have gotten the offenders kicked out long time ago.
3. Is the character consistent with 1960's history and culture? Or at least the Hollywood version, since TF2's version of world events seem rather different than what happened in reality. I tend not to care about the classes political, religious, or cultural leanings as much because discussing those topics are controversial and I couldn't really do those topics justice without an amount of research that I don't really care to do for pretendy fun times. But I'm not above assuming things like Spy wearing sock garters because that would be a rather in-character thing for Spy to do, if only because he's supposed to be a walking French stereotype.
4. Can the backstory be handwaved as "because it would be funny"? This is pretty much what I use to flesh out the rest of the characters. Did Sniper have a wife whom he beat to death with a golf trophy, probably not, but it makes for amusing headcanon, so sometimes I have that as backstory, sometimes I don't. Is Demoman a conspiracy theorist who thinks the Illuminati are plotting world domination? Considering his obsession with the supernatural, why not? Maybe the Illuminati even actually exists in TF2-land. (Though, personally, Soldier seems more the type to believe that the local water supply is laced with LSD or what have you.)

I pretty much judge all TF2 characters, regardless of how "close" they may be to canon, by those standards, so even if they fail on some criteria, I don't dock the story points if it's still a good (or entertaining) story, but I definitely grade characters on how "standard" they are.

Even with my own RP, when I was in Mayfield I considered my Sniper somewhat non-canonical because I added the following (among other things) to his backstory:
1. At least one of his parents are British, and he was born in Great Britain before moving to Australia. (Blame Zero Punctuation. I'd made this up before Valve told us Sniper's last name is "Mundy", so I gave him the last name of "Croshaw"--but just in case, I decided that this was an alias. It pays to be prepared.)
2. He was sort-of married to a girl who left him. (Inspired by that line from "Meet the Sniper" again, because it makes for delicious angst.)
3. He had a Friends With Benefits relationship with a RED Spy (notice I use "a" and not "the") before said Spy was abruptly transferred out of the team. (This one was purely because I was shipping Sniper/Spy a lot harder than I do now.)