Today, I learned you are just supposed to set a config option to turn it off (go figure - I don't know if this is new or if I just never looked hard enough).
Anyway, here's the info in case you want it.
Just set the option gui.gcwarning to false.
Do it like this:
git config --global gui.gcwarning falseIf you're interested how I was doing it before (you really shouldn't be but in case you're curious) - under your git install folder there's a file somewhere (probably called git-gui.tcl) that makes a call to a function called hint_gc that is the function that shows the annoying message. I just commented out that line in previous builds. Now, I see that it checks a config variable, but I guess I either didn't notice or it didn't used to check.