There are at least two tools which attempt to mitigate the pain on online shema modifications - both by big hitters in the MySQL world. One is pt-online-schema-change from Percona and the other is oak-online-alter-table from Shlomi Noach. Could depend on whether you're more at ease with perl (percona) or python (Noach).
Needless to say, I urge you to test before implementing a solution on production.
It's unclear as to which of the toolkits (or which particular tool, if any) works with Windows - no mention of an install for oak-toolkit - there's one mention of Windows in the 366 page Percona pt-toolkit manual. In any case, for Windows, an install from source appears to be necessary.
There is however a tool by Facebook called OSC (Online Schema Change) which is a PHP script - could be suitable for Windows? Windows isn't really my thing, but there's an article here.
There's yet another solution available here - it involves replication, cutting over and cutting back. Appears to have the advantage of working under Windows. Again, you can test (and YMMV).
Found something even better - here. Fromdual are big on the MySQL scene. You're on 5.6 so this should apply.