My wife and son got the 4.4.3 update notification on each of their 2012 Nexus 7 this morning. I told them not to install the update; I'll handle it when I get home this afternoon. My 2013 Wifi-only Nexus 7 needed to be on stock recovery in order to install the 4.4.3 OTA, so I assume the same is true for the 2012 Wifi-only Nexus 7. I'll do the same that I did for the 2013 N7:
1) restore stock recovery, 2) adb sideload the OTA or just install it from the tablet, then 3) re-install custom recovery and re-root.
Update: I installed stock recovery, then tried to download and install the update on the device, and got an "Error" message with Android on its back and an exclamation point in a red triangle. I long-pressed the power button to reboot and it's still on 4.4.2 and says it's up to date.
So, I downloaded the update to my computer and tried an adb sideload. When I did that and watched the update fail I saw the detailed error message that "/system/bin/debuggerd has unexpected contents". Probably something from an app requiring root. So, I downloaded the 4.4.2 factory image from the google developer's site, used 7zip to extract the system image file and flashed it to the device. After that I was able to adb sideload the update, then reinstalled TWRP. When I tried re-rooting using NRT, there was no SuperSU on the device, so I installed it from the Play Store and when I opened it I chose to install binaries through TWRP. When it booted into TWRP it immediately began flashing an old Titanium Backup file named "update.zip", which I did not want to happen. That screwed up a couple of apps, but nothing that couldn't easily be fixed. My lesson is to not leave any files named "update.zip" in the root directory.