Yes, you can mix WordPress and non-WordPress together. You just need to be careful of files and filenames, as well as URL rewrites. You’ll also need to consider file structure so you don’t have things stepping on each other.
The ideal in my opinion is to maintain WordPress in a subfolder. Note that that is not the same as running it in a subfolder. I’m just talking about where the files go. That way you’ll keep them separate from anything else you are doing. See Giving WordPress Its Own Directory in the Codex for more info.
You probably will need to run WP in a separate directory as well (aside from what I mentioned above). This would be due to the loader scripts in the index.php file. That will probably conflict with the other CMS if you try to run them from the same URL. You might be thinking “that doesn’t make any sense,” but keep in mind that multisite will make the subsites a directory lower than the main site.