That is still a very good team, and you could park the bus, play on the counter etc. It is not over by any means. In fact the odds for the tie only changed a little bit (from 3.55 for Bayern to win the thing, to 3.7)
Plus, Lewandowski may in fact play. Ribery might even play. So, who knows? In any case, and as good as Robben is, he is not as crucial as Messi is for us, nor is he nearly as good. You also have a bigger squad than we do.
So, Robben is the only grave absence for Bayern in my mind. He is someone they cannot really replace. Alaba is great, but Bernat is good as well, a LB is not that crucial anyway. Ribery is a big name in football, but either way he is getting old, he is not the layer of 5 or even 2 years ago. I am not saying he will not be missed but he is not as crucial anymore.
And yes, we would be the favorites even if Bayern had zero injuries, not massive favorites for that matter, but favorites nevertheless.