If you are unable to disable the included apps using the built in application manager, then your next best option would be to root and freeze them with Titanium as mentioned. Once you do that, you will likely not be able to apply new firmware updates because you are changing the default system when you freeze apps. If future updates DID apply, you may be left with a phone that does not boot properly.
I believe several, if not all of your issues are related to the fact you're using a Korean phone in your location of Pakistan:
It seems the term "international" is slightly misleading as related to the G2. Though it will work in multiple countries, it won't necessarily be optimized for your specific location because there is a large number of firmwares for the D802 that have slightly different content based on locality. So the short answer to all your questions is that some of the issues, you may have to live with and use workarounds as necessary unless you can locate a firmware specific to your country/region. I have not seen a firmware specific to Pakistan in my travels around the internet, but it could exist I'm not sure.
At minimum, you could root and disable the unwanted apps however. That would help with some of what you are dealing with including unnecessary CPU usage and virus detection when connecting to the PC, provided that the virus detection is being generated from one or more of the pre-installed apps.