Turns out you can upload zips manually. Since Curseforge and Wowace don't yet support patch 7.x, you'd still want to put a note in your main description, preferably with the date.
Something like:
May 16, 2016
All zips created on or after this date are for the Legion expansion or 7.0.x pre-expasion patch, and will not work with live Warlords of Draenor servers. This starts with MyAddOn version 1234 and newer.
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The Curse Client will update to newer versions, but if people can't or won't read, you aren't to blame!