To be honest, people farming the achievements in game harms the game a lot more than people just unlocking them out of game. A lot of the achievements are just downright pointless and don't make you deserve the weapon anymore than someone who used an application. (This was much more evident on the medic, heavy and pyro achievements, but my point still stands).
Some examples (Take into account that the scout ones are better than the older ones):
1) Destroy 3 teleporter entrances - A spy should be doing this if he can be bothered, it's not really an achievement to destroy a defenceless building 3 times
2) Kill a heavy then eat his sandvich - Most heavies don't use the sandvich, you might as well rename it to "Find Murk while he is injured"
3) Do 1000 double jumps - What the hell? Why should I?
4) Kill 4000000 enemies from behind with the FaN - Maybe if it was a viable weapon
5) Capture the intel 30 times in one game - Most people will not be able to do this without just going onto a empty/near to empty server, I challenge someone to do this on a 28 slot server.
I unlocked 13 achievement in-game (I wasn't helping the team in anyway, since the achievements which you can do without the new weapons are crap), then just got bored and unlocked 7 ridiculous ones with the application.
If you think that destroying 3 teleporter entrances is fun...
