like xflak said, use modmii, I use it, thousands have with no virus. your getting a false positive.
As for running on linux, try wine or vmware, otherwise, use a friends/relatives computer running windows
Is there any other way? i really don't feel like taking any risks with my computer system
There are other ways, but if you consider modmii "taking a risk", then they all pose the same risk with either your computer system and/or your wii.
On the plus side: there is little to no reason to upgrade in the first place. Just go ahead and
check the version history of the wii menus. There's hardly anything to gain, and games flat out lie when they say they "need" to perform a firmware update (though that only becomes apparent if you actually block the message from showing up).
BTW...What virus scanner are you using that you (apparently) get a warning? I'm using avast and it never even blinks.