Yes, they will be completely fine. It fact, you should be extremely grateful you have PokeRus. It's actually extremely rare and very useful, especially if you want to train Pokemon for competitive battles. It has no negative effect on your Pokemon at all.
What it does it doubles Pokemon's Effort Value intake (click the link if you don't know what they are, the page will hopefully explain it). The virus doesn't last forever though, and once the Pokemon has been cured of the virus it can never be infected again. So make the most of it, and if you want to keep it around put your infected Pokemon in the PC! They will never lose the virus in the PC.
The virus will spread to your other Pokemon eventually, so you can probably just spread it to something useless you won't use like a Pidgey and put it in the box, so you can later take it out and spread the virus again it you want.
To give you an idea of how rare it is, every wild Pokemon has an extremely low 3 in 65,536 chance of having PokeRus. That's almost three times as rare as Shiny Pokemon! And to make it even harder to find, you will only get the virus if you KO or catch the Pokemon with it; if you run away from it you won't get it. So you're really lucky!
More info on PokeRus if you want it.