Well,
Don't turn the power on and off too often in a limited time, as it may damage the computer. Allow the computer to rest a few minutes between each session.
If none of your disks contain personal data you want to keep, don't spend time removing viruses from them. Formatting them or copying another disk (or disk image you find on Internet) on them will remove any virus anyway. However some of your disks might be restored by the "install" function Thomas described. If these disks are original they may be worth restoring, as copies you will find on Internet are mostly pirated copies. But instead of turning the computer on and off, you should first find and use a clean Workbench disk, run an anti-virus program in the background, such as Virus Checker, and then "install" these disks. Thanks to the anti-virus running in memory you won't have to turn the computer off in order to clean the memory.
Some disks may decide to run when you remove the protection for various reasons, but any clean game should work on a protected disk, so keep your disks protected unless you want to write something on them, or clean them from viruses using an anti-virus - or the install command if only the bootblock is infected.
Yes the easiest way of cleaning a disk is to use another clean copy of the same software. If your game is an original disk you may be unable to find an exact copy of your original, since most available copies are pirated copies that sometimes have altered the originals : in that case using WHDLoad may be a solution if you have a hard drive.
Even if you were able to connect the Amiga to a PC, you need at least a Workbench disk in order to connect the two computers, so I advice you to buy a working Workbench disk on eBay, or we may send one to you. Then buying an old PC with a serial port is a cheap and versatile solution. You may as well transfer files using the PCMCIA port of your Amiga 600, but I'm not a specialist. If you have a hard drive, the easiest solution is to plug your Amiga hard drive into the PC and copy files on it using the WinUAE emulator.