Using lower resolutions on MacBook Pro Retina a good Idea?

No the performance would, if anything, improve if you use a lower resolution. Although I can't seem to understand how the retina MBP would give you more eyestrain at 1440x900 than your old 2009 MBP at the same resolution? If the problem is the pixel density then it wouldn't matter if you run the screen at native 1440x900 or 1280x800. You would still have the same amount of pixels running (2880x1800).

Well my answer to your question is; no the performance will not be affected.

Okay, so you had the 13". I thought you had the 15". But if you run 15" at 1440x900 then everything is the same "size" on the screen as on the 13" but with larger screen real estate. So you shouldn't have more eyestrain at 15" 1440x900 than 13" 1280x800. I used to have the 13" 2010 and I'll have to say that the 13" gave me more eyestrain than the retina one (because of the lack of pixel density). Hopefully you'll get used to retina display!