Preventing iTunes from keeping old versions on "Mobile Applications" folder
I don't know an easy solution to change iTunes, but I do have a cleaner library by letting go. It's not exactly what you ask, but here goes anyhow.

I did one good backup of my user folder and then deleted all apps from within iTunes. Then I cleared out the folders to remove any left over / orphan app files.

Then I connected my devices one by one and just transferred the purchases. Less updates of un-needed apps and less space used.

I suppose they could pull an app from sale and I might miss out on some updates, but I'm willing to take that risk. I've still got the last version I wasn't using stored on my backup.