If the devs were at war with mods then modding would be way more difficult than it is. If you don't want mods breaking on update then you're just gonna have to wait for the game to hit V1.0 and hope they don't do any further updates on that, which is unlikely because there's gonna be bug fixes.

Edit. Also, if you got mods installed that you don't want breaking then you should turn off auto update for the game. Whenever an update is released you should then check the mods online to see if the mod creators have updated them for the newest version, if so then you'll be free to update.