I have run this game on Win7 for quite some time with no issues, so it isn't a Windows 7 specific issue. My installation of Windows 7 was built specifically for playing this game, and I had no other programs installed, and had it streamlined in order to prevent background programs and services from running.
The trick with this game is to free as many resources as possible, in order to allow the game to run uncontested. Drivers can be a bit tricky with Win7, I would recommend making sure you have the newest drivers that are compatible with 7, and search the threads here for optimizing your experience for other tips on smoothing things down.
Not sure what you refer to with the virus situation related to the flash upgrade, if you need help with that please post some more details. The flash installation itself is safe, but ifyou aren't completely secured, any download could invite virus's based on pre-existing circumstances.