The simplest solution: you can store the initial version number of the game at installation in PlayerPrefs. Then when you add the ads, you can have a check of the minimum version number versus the initial version number. Or you can record in PlayerPrefs whether it is a paid version or not on the initial launch again.
That leaves some problems: what if someone uninstall the paid version and reinstalls the free version? You might need a way to grant them the "no-ads" flags remotely. I use in-game gift codes for that, but it requires a backend of some sort (using parse.com).
It is also susceptible to hacking of the local data, but if someone is willing to go to that length, it doesn't matter what you do - so don't worry about that.