Of what I'm reading from your question, this is something a lot of websites are having issues with. "What happens when our search results are less then the amount of filters filling our page?". For that some great examples of online solutions can be found. In a company i'm working on, we have been struggling with the same question.
First of all, if your website / application is already live. Be sure to do a research of which filters are the most used filters. If you can't do that, make assumptions which you will test on a later stadium. Your most used filters, will be filters that are default open to a user. All other filters can be collapsed, and opened by a user.
Something else to consider is to avoid the use of scrollbars. Not only will it look disturbing in a design, it kills the overview for a user. Therefore, choose to only show a few filter options (again research which of these are most used). Let a user either search for it, or click to open more.
With this said, a user then accepts he is making his filterbar longer then 'necessary'. And also knows his results can be found on top of the page. Your design could then look something similar to this:
One other thing that could really help is, when a user has scrolled down so far, his search results are not visible on screen. Notify a user something has changed and he needs to scroll back to the top. Make it even more easier for him, to add a click functionality on that notification. Only show this notification when a user changed something to his filters. For example, activated Filter 7, Option 2.