There's simply no evidence that Glee is in trouble, IMO. Not ratings, not critical response, not outward indications of network support.
(BTW, Joss Whedon is going to direct one of the back nine episodes.)
Ratings week to week -- fast nationals, not finals, WITHOUT DVR numbers, the first numbers are 18-49 rating/share, second number is total viewers (in millions):
Shomance, 9/9: 3.4/9, 7.1
Acafellas, 9/16: 3.1/8, 6.6
Preggers, 9/23: 3.0/8, 6.6
The Rhodes Not Taken, 9/30: 3.2/9, 7.3
Vitamin D, 10/7: 3.2/8, 7.3
Throwdown, 10/14: 3.3/9, 7.4
No question, there was a dip after the first regular episode, but since the Kristin Chenoweth episode, the show has been steady, even slightly improving week to week. And even wth Preggers, the lowest-rated episode (and premiere night on the competing networks) Fox still won the night in 18-49 year olds.
Glee has also been scoring significant gains when DVR +7 data is added in. The Rhodes Not Taken went up to a 4.2 in the demo and 9 million total viewers, a 27% increase.