Magic Window causes GfxCardStatus to switch to Discrete mode
Yes, I'm afraid it will have an impact, but not necessarily a big one. I'm in a similar situation, a seemingly-benign app (Postbox, a mail client of all things) forces my discrete graphics on too (same model, MBP Retina).

The authors are fully aware of it but say there's nothing they can do - ultimately the choice about whether to enable discrete graphics is up to Apple, it gets turned on automatically if OSX detects that heavy graphics processing is taking place.

Apparently in the case of Postbox it's due to font rendering or something. I've just learnt to live with it - if I was really desperate I can force it back to onboard graphics using the very tool you mention anyway.

How big the effect is really depends on what the application is doing, and only you can determine it, by trying it with graphics first on discrete and observing estimated battery remaining, then again on integrated graphics. This should be a reasonable clue.