Then the solution is simple. Don't use that folder.
Better yet, don't use a modpack launcher at all. While I'll grant Magic Launcher and the like are useful, all you really need is a backup of minecraft.jar, a text editor, an archiving tool that can open minecraft.jar and a little patience to be willing to change your ID's and/or mods to the settings of whatever server you're logging into are. Then you avoid the issue entirely.
Granted, that causes problems when trying to distribute modpacks, but I see that as a minor inconvenience I can put up with. By running with only the default launcher and those things above, I have the freedom to run whatever mods I want, at whatever versions I want, with whatever config I want. I'm not restrained to whatever Minecraft the launcher uses (Such as for example the long time Technic was stuck at 1.2.5), I'm not restrained to someone else's idea of what the best combination of mods are, I can up or downgrade both Minecraft and the mods as I please - in short, I find things better without a custom launcher.
I just use Magic for the convenience of it - and I don't suffer from the problem you do.
This is the problem with modders you really only have two option either the slowpoke vacation fund aka FTB or do stuff manually and hope that both you and yours fixed all the item ids the same way in order to play together. But this will also happen with minecraft.exe