I am very happy with my 7d and use it for astrophotos as well. As long as I use post processing (stacking , noise reduction) I can go up to 3200 or sometimes even 6400 ASA to get a decent low noise.
But for time lapsing I need a lot of pictures which are grain refined in itself because the camera has to take every 20s ... 1 minute a picture using a time lapse controller such as an Aputure cable release or an Android device with the DSLR controller app.
Even when setting the C Fn II Image => Long exposure noise reduction to ON and High ISO speed noise reduct'n to STRONG, the pictures are rather grainy even at 1600. Strange, pictures taken indoor @ 3200 or even 6400 are less grainy when when the latter setting si set to NORMAL.
OK it can be removed by Photoshop, GIMP or DPP, but when I have hunderds of pics to be grain-refined manually that is not an option.
Here an example of a 1600 iso pic of 1 second.
What am I doing wrong ?
I would be turning long exposure noise reduction off and changing high ISO noise reduction back to normal or disabling it entirely. While I have no experience with the 7D, with my 5D mk II and 60D cameras, having particularly the high ISO reduction on visably reduces the quality of the image. This may be the cause of your issue. For individual shots you are better of doing noise control in post processing like you say you have. Timelapse movies are very forgiving on noise in the individual images. It barely shows up in the finished film.