Well, I hope not, since I absolutely love the eye control, even on the tiny EOS 50e with its three AF-sensors. In my opinion it's the best invention for autofocus cameras ever and the only sensible way to use AF... what good is it if you spend all your time selecting the right points with tiny buttons while you could be taking pictures?
Anyway, the amount of IR-radiation is even less than what you get from normal daylight or looking into the sun for a few milliseconds, so I don't believe it does any serious harm. Everyone's eyes age, no matter what the concrete circumstances are and the percentage may be a little higher for photographers, especially when they spend a lot of time staring into tiny viewfinders.