The Autumn class is OP if you find the Mother of Intervention. From a balancing the Autumn perspective is there any talk of giving the Covies an ability similar to the Autumn except disabling/ destroying a ship ala boarding craft?
No.
Autumn-class with shields?
Late game UNSC sub-faction research. I'll let Rovert go into more detail if he so pleases.
It actually depends on the information that comes out about the Autumn. Currently there's no indication that they have shields - if a canon source says they do they'll probably have effective shields even without the research
And then the Autumn will be completely rebalanced cost wise.