I was in a similar situation, but I choose the non-IS 100mm macro lens because of similar (or slightly better) overall IQ and I will keep the 2.0 100 lens:
first time i hear that the non L version has better IQ... i highly doubt that.
every review i have read so far tells the L is slightly better.
equal maybe but the non L better? that is stuff people tell themself so they don´t have to buy the more expensive L lens.
A late reply but now it's there
APS-C comparison between both (50D) (1st is NON IS version)
FF comparison (5D mk ii)
The differences are marginal - but the NON IS shows much lower CAs and a better uniformity of sharpness which is important to me because I like compositions where sharpness is needed at borders/in corners @ f/2.8 or similar.
As Hesbehindyou remarked - sample variations play an additional role.