Generally speaking, as long as all AP's broadcast the same SSID with the same authentication method / credentials, there is no inherent problem mixing and matching AP's from different vendors. Clients choose which AP they want to talk to, and everything should be 802.11* compliant so the client doesn't know the difference. Note that the ZoneDirector won't know anything about the Ubiquity AP's, nor will it care. And similarly, Ubiquity won't know anything about your Ruckus hardware.
On the flipside, it makes it harder for you to debug user complaints. You'll need to search two sets of tools to see which AP the user is on and how they are roaming across them, etc, as well as narrow down problems with two heterogenous configurations.
Nothing like that really exists on the market for a "universal" controller that provides centralized control of AP's from multiple vendors.
I strongly recommend standardizing on either Ruckus or Ubiquiti AP's (I would obviously recommend Ruckus as the technically superior choice if your budget allows), or just forgoing the requirement for one-controller central management.