Can't you do /fly on or /fly off or is it just one command (/fly)?

Because if you could, you could make a clock activating a command block with "testfor @p[r=(how many blocks away from the command block you want to disable flying),ml=0]" then connect it to a comparator and connect the comparator to a command block with "fly @p off"

Just use command blocks and make it so the player cant teleport out of the map whilst in the map. for example Player enters a region they start in a room which has a "Back to spawn" pressure pad which sends them back to spawn and a Door with a pressureplate that enables fly on the player and that leads to your parkour area and when they jump on the leave pressure pad they have their Fly rights stripped from them and teleports them to spawn
(Something like that)

I can help you with ANYTHING WORLDGUARD and I have nothing to do at the moment so I would be happy to help you and setup a region that does exactly what you want it too do (I'm a experienced with World Guard)

/testfor the player 4blocks above the platforms and teleport them back to a checkpoint with the message NO FLYING ALLOWED!! That should work.

For this, you have to use world edit and worldguard. A feature, "flags" can be found in worldguard to block commands in desired areas.

1) Select the area you want to block a specific command using //wand.
2) Expand the region vertically using //expand vert
3) Define it as a region using /region define <Parkour>

To block commands use /region flag Parkour blocked-cmds /fly

More commands can be blocked at the same time by adding a comma after a command.

Disclaimer: This is 100% original
Example: /region flag Parkour blocked-cmds /fly,/tpa,/tpahere