Do I really have to apply Mirror Modifier before I go rigging?
There is “vertex groups” option under Mirror Modifier. Is it possible to use it so that I can keep mirror modifier and still animate both sides individually?
What you do is make a duplicate of your mesh (as mirrored) and save it on a layer for if you need it later. Then on the other one apply and rig.
>> Is it possible to use it so that I can keep mirror modifier and still animate both sides individually?
No, if you want each side to be animated differently, you need some real vertex’s there to be in a group to modify with the armature.