May not be the most "robust/elegant" way, but as a pointer, I am using shell_exec to accomplish this (with Imagick installed).
...
shell_exec("convert '$flyer->file'[0] -colorspace RGB -geometry 200 -flatten '$flyer->thumbnail_path'");
$flyer->save();
Just make sure that the paths for both $flyer->file and $flyer->thumbnail_path are defined beforehand.
The back-ticks around $flyer->file and $flyer->thumbnail_path, are for filenames with spaces (learned the hard way).
While it works, I personally am not fully happy with this, as it is not fast enough, IMHO. If looping through several PDFs, it may take a few good seconds.
The way I would like this handled is in background, but I need the thumbnails on the next view after "Save" - so this has be handled at this point.
If anyone has a better solution, please comment.