They (Bayern Munich) will not be hampered only by Manuel Neuer, because they still have Sven Ulreich who is also a great goalkeeper. For SC Freiburg, i'm not surprised to see their good performance this season, because last season they were even able to finish in sixth place in the standings.
Sven Ulreich before joining Bayern Munich had defended two great clubs VfB Stuttgart and Hamburger SV, with the experience he has of course Bayern Munich's goal will still be safe from conceding. However, SC Freiburg seems to be having a bit of trouble in the bundesliga this season because many of their players have been injured, such as Manuel Gulde, Kimberly Ezekwem, Jonathan Schmid and Merlin Röhl. But I'm sure SC Freiburg will continue to appear consistently as Bayern Munich's rival this season.
The continuation will be happening in a month from now and i guess that those players who got injured may able to perform in the bundesliga again. Some players like neuer got serious injury on his leg and he will not even able to perform maybe until the end of season but he will be coming back again next season. Sven's only playing in three match in total since the early season till now. I hope that bayern will try to consider him as he can also doing so well like neuer to protect bayern's goal.