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Imagine this: You are in a ranked queue and waiting to start the game. Meanwhile, you are browsing the internet. You are done with your page and hit Cmd+W to close the window. Instead, you quit LoL client and get a leaving game penalty.
There are multiple things wrong with this scenario, all of which can be solved sticking to once simple philosophy:
Cmd-W: Closes windows, never quitting an app (Which means LoL would ignore this)
Cmd-Q: Quits an app
Search apple's KB page for "-W". You'll see 5 results. Under one result (Specifically Cmd-Opt-W for closing all windows instead of 1) it mentions that it will close all windows without quitting the app. Clearly the implication, and my experience from being a mac user for a dozen years, is exactly as I stated above. Cmd-W should never attempt to quit an app.
Please understand, I am frustrated as this is at least the 5th time this has happened. I can't be alone on this one. :] Should be an easy fix.