A couple things, you could create your own custom smart search index and have a custom property on the page types in addition to "exclude from search".
Secondly, if you have a specific node or children you could simply exclude them in your index. But by the way it sounds, they are just random pages so that may be a little more difficult to manage if you're doing that for every page you want to exclude. Then again, I don't believe this will get everything you need accomplished.
Lastly, you could modify the system files, not recommended.
I'd go with option 1.