The whole point of a solid-state drive is to decrease application loading times, and that's it for most users. That being said, if you only care about loading subsequent programs (or logistically prefer keeping your OS separate), you can easily keep the SSD as a secondary drive, only using it for certain programs/tasks.

That being said, if you perform any operating system related task that needs to retrieve data from the drive, it will be much faster then if your OS was on the HDD. You are correct, your OS will only boot up faster with a solid-state drive.