if you said something like "the malware definitely won't damage your recovery console/partition" i would run the recovery console. the ultimate goal is to have a secure computer.
I would not say that, because it may not be true.
My understanding of the recovery process, (at least in Emachines), is this, If you are in possession of the discs, you can take a new, blank hard drive, and using the "destructive restore" option you can, format the HDD, and recreate the recovery partition. The "repair" option loads a fresh copy of Windows from the existing "D:/" partition. All manufacturer's strategies are not the same, so I am unable to make a blanket statement about this. In fact, in another thread involving an Emachines computer, the OP said the recovery discs did not even offer a "repair" option, it was destructive or nothing.
Since the discs also carry the driver set, which is correct and contemporary of the date of manufacture, everything will work as is should, without resorting to an internet scavenger hunt for software that may be unavailable, or not compatible with the OEM board.
In any event, I suppose the issue is time as opposed to money, or even time and money, in tracking down recovery media. I personally would feel uncomfortable in owning a machine that I did not also own its recovery discs.
IMHO, as the old saw goes, it's "six of one, or half a dozen of the other", but starting with a machine that there is nothing of personal value to lose, a blank slate as it were, I would have wiped the drive, hunted down the recovery discs and started over. Is it worth 30 bucks to be certain of what you have, I say yes, but I'll qualify that by saying it is if you have the thirty bucks.