If the cage is rubbing, make sure it is adjusted right.
I haven't used Di2, but it should be similar to other derailleurs. Typical adjustments are:
Vertical + right/left pivot at the mount.
High Stop
Low Stop
For mechanical, you also have cable pull/indexing.
For mechanical, when riding, one can often also "trim" a bit.
If it is truly bent, then as above, with a little patience, one can often straighten the cage.
An option might be to look to see if other cages such as Ultegra mechanical cages look the same. My guess is that the Di2 will use its own cages, but it is worth looking. If the cages are the same, then it might be simply a matter of removing and replacing rivets.
In some cases, one can also downgrade parts like a cage, so if you're running Dura Ace Di2, it may still be compatible with a lower quality (cheaper) cage.