Several varying themes in your post, so I'll try and address what I can.
Yes, conditions have been a negative factor against absolute performances at several recent major events. However, everyone is affected, even if some more so than others. Someone with a 2:16 PB is not going to suddenly medal just because the heat/humidity slowed the medalists to 2:15 - 2:17 range.
And that line has been drawn. The IAAF came out with one set of standards, making the marathon times significantly easier, relatively speaking, than the rest of them.
Athletics Canada, under direction from the purse string holders at the COC, uses the same IAAF standards except for the marathon, where the domestic standard is toughened to be closer to equivalent to other events.
Neither the IAAF nor the AC standards/criteria do I see any room for exceptions to those lines ('they were just 3 seconds off standard, so let's let them compete anyways), so I don't think one can claim any kind of wishy-washiness. The line has been drawn.
Granted, like pretty much all lines, not everybody likes where it has been drawn. Some people feel that just being in the top 400 or 500 marathoners in the world should be good enough to go to the Olympics. Others feel it should be more like top 100. Neither position is absolutely right or wrong, although all other events require the athlete to be pretty much in the top few dozen to make Olympic standards.
1) Why do the Olympics have to be the be-all and end-all? If someone isn't fast enough for that event, what about qualifying for Commonwealth, Francophone, NACAC, etc?
2) Again, define 'anything'. Has any 2:16 or slower marathoner ever placed in the top 12 in recent Olympic or World Championships?
3) See item 1). Marathoners also have the advantage of great competition at London, Boston, Chicago....
4) Aren't the 5000 and 10,000 distance events?
5) The COC is certainly not infallible. I'm curious though as to how much of their funding is public money versus corporate sponsorship. To whom are they really accountable to?
I'm not really sure what point you are trying to prove with the examples of Eddie the Eagle or the African non-swimmer who almost drowned in Sydney (that's entertainment?)