I think it's either-or in this situation, then, and you can go with whatever version you like best. The idea of a threat to Kennet and Niki that Kiril must remain with them to defeat seems more compelling to me than just hearing that he has to go on living as a nameless ghost among aliens, which seems more of a static thing (sad, but static) with no imminent hope of resolution. However, if there isn't actually a big threat to Kennet and Niki once they're rescued, then the original version might be a little misleading.

I don't think I can help any further without actually reading the book, but I'm glad you feel my comments have been of some use to you in the end!