Hey everyone & unclesol,
hope I can help you with this... a month too late, but I myself figured it out just a couple days ago...
I'm still a beginner, so excuse me if it's too detailed. Maybe another noob like me might find it useful
I also wanted to encrypt my rooted phone (Note 3 N9005) but as OP said, encryption cannot start and crashes due to root being activated. The bad thing is that you cannot root after encrypting (as far as I know...).
Sometimes deactivating SuperSU temporarily (settings -> application manager -> SuperSU; don't tick deactivate-box in supersu app) and start encryption in safe mode helps.
But when it doesn't you can do it like alphahere from xda suggests. Here the steps since I may not post the link to his instruction
1. According to him latest busybox needs to be installed.
2. After enabling USB Debugging on your phone, you need to go to adb shell on your PC and type su for root access . Accept the root permission request on your phone. You will then see in adb that the $ will turn into # . (That's what took me so long to get it right as a beginner

)
3. Type following command: pkill -KILL daemonsu
This will temporarily disable supersu/root. (You see that the # will turn back into $. Also you'll see your apps won't be able to gain root access). After encrypting your phone will be automatically rooted again.
4. alphahere says not to open SuperSu afterwards. Just start with encryption.
This time encryption won't crash (at least it worked for me on BobcatRom and X-Note Rom). Yeahiiiii
Some other collection of tips/apps some might find helpful AFTER encrypting:
As much as I love encryption on my Galaxy, Samsung forces you to use the password lock option with at least one number and the PIN option is greyed out. On the one hand you need a long password for security but on the other hand it's a real pain to type that long PW everytime you turn on your screen.
1. For those of you who cannot run the app "cryptfs" in order to separate boot PW and lockscreen PW, you can do it manually (Found it on Nikolay Elenkovs blog, big thanks!):
- As above you need to go to Adb Shell. Type:
su -c vdc cryptfs changepw newpassword after the $ symbol and it's done. Other users warn you that the maximal length should be 16 characters. Otherwise bad things will happen...
2. The step above does not solve the enter-PW-everytime problem.
On my Samsung, in settings you can disable the lock for max. 30 minutes, but then there is absolutely no lock, not even swipe... annoying when you accidently hit a button in your pocket... The app "delayed lock" solved this for me. A widget on your homescreen can let you switch between your password lock and swipe lock.
3. I found this awesome app "Remote Power Off" on xda. You can turn off your device remotely by receiving a SMS with a certain code you chose.
Nice if you forgot your phone somewhere ... I think

(When you notice your phone keeps shutting down after receiving a SMS, changing your code can help you with this)
Happy October Encryption Time For Yall
