In the Debian boot system, several packages include scripts that are started from /etc/rcS.d/. In fact, there is a bite more of them than make sense, and this causes a few problems. What kind of problems, you might ask. There are at least two problems. The first is that it is not possible to recover a machine after switching to runlevel 1. One need to actually reboot to get the machine back to the expected state. The other is that single user boot will sometimes run into problems because some of the subsystems are activated before the root login is presented, causing problems when trying to recover a machine from a problem in that subsystem. A minor additional point is that moving more scripts out of rcS.d/ and into the other rc#.d/ directories will increase the amount of scripts that can run in parallel during boot, and thus decrease the boot time.
So, which scripts should start from rcS.d/. In short, only the scripts that _have_ to execute before the root login prompt is presented during a single user boot should go there. Everything else should go into the numeric runlevels. This means things like lm-sensors, fuse and x11-common should not run from rcS.d, but from the numeric runlevels. Today in Debian, there are around 115 init.d scripts that are started from rcS.d/, and most of them should be moved out. Do your package have one of them? Please help us make single user and runlevel 1 better by moving it.
Scripts setting up the screen, keyboard, system partitions etc. should still be started from rcS.d/, but there is for example no need to have the network enabled before the single user login prompt is presented.
As always, things are not so easy to fix as they sound. To keep Debian systems working while scripts migrate and during upgrades, the scripts need to be moved from rcS.d/ to rc2.d/ in reverse dependency order, ie the scripts that nothing in rcS.d/ depend on can be moved, and the next ones can only be moved when their dependencies have been moved first. This migration must be done sequentially while we ensure that the package system upgrade packages in the right order to keep the system state correct. This will require some coordination when it comes to network related packages, but most of the packages with scripts that should migrate do not have anything in rcS.d/ depending on them. Some packages have already been updated, like the sudo package, while others are still left to do. I wish I had time to work on this myself, but real live constrains make it unlikely that I will find time to push this forward.