As far as i can tell there is no way to change the theme of git-gui as packaged in git for windows without editing .tcl files.
When you use the Git GUI here context menu option, the .tcl files that are interpreted are those in C:\Users\USERNAME\AppData\Local\Programs\Git\mingw64\lib\tk8.6\ttk. You can confirm this with Process Monitor. You'll want to filter for wish.exe if you do so. Oddly enough there is a totally separte copy of these files in Program Files/Git.
A .tcl file that git-gui interprets directly is ttk.tcl. To demonstrate that this is the case add the following line ttk.tcl somewhere at the top level.
tk_messageBox -type ok -icon info -message "Hello world" -title "Info"