I would like to do a company-wide survey, but I don't want to import all 6000+ emails into Limesurvey. I however need to restrict paticipation from the same user twice. Is it possible to do it without providing the emails?

The only reliable way to restrict participation is with tokens.

It only takes a few minutes to import thousands of tokens via CSV.

Like Tpartner. If the issue is the work to import them, than this won't take you more than a couple of minutes. Preparing a CSV file with the emails should be quick.

Now, if the concern is uploading 6000 email addresses to a tool in the cloud, you could approach it differently.

You could just create dummy tokens with fake emails. You can then create token links in Excel pretty easily and you can send personal links including tokens to each employee through your internal email system. This still will give you control over the number of times a link can be used, but you won't have to upload any real email addresses.