Yes, the AfD will almost certainly enter the Bundestag - but not in such numbers as to get anything done. With a bit of luck, the FDP (by far the most free-market party in Germany) will also make it back into the Bundestag after narrowly dropping out last time. The far bigger threat to Merkel is that she's lost most or all of her lead over the Socialists, led by Martin Schulz who spent most of his political career in the European Parliament. She might not remain chancellor indeed, but then she'd be replaced either by a Socialist, or by someone else in her own party who would govern with the Socialists.

As for Wilders' weak score being 'too bad' - I doubt you'd say that if you saw the full picture about him.