Play Store updates downloaded on 3G network by ignoring settings
If you haven't done so already, try going to Settings - Data usage, then press the menu key and choose "Restrict background data".

This sets all sync functions to only work on Wi-Fi, maybe it also helps with your Play Store problem. Be careful though, if you rely on sync to work even when you are not on Wi-Fi (Gmail for example), this is not the right option for you.