Hi Ottis,
Without knowing more about the specific use cases for your extension, it's hard to say anything for certain here. Our policy focuses on us being able to understand the functionality and full capabilities of your extension.
We don't have any automation that would immediately ban an implementation like this, and for accidental violations of the remote hosted code policy you will usually be given time to make required changes.
This said, using that approach to run code especially if the user has not enabled the extension in incognito could be a concern. Ultimately I think you need to think more about the spirit of the policy here. If you're building a bookmark extension and you want to open a bookmark the user has which is a javascript URL, you are probably fine. At the other extreme, using it to unexpectedly run code in incognito that the user isn't expecting would almost certainly be a violation.
I hope that's helpful.