I thought of this too – I am kind of hoping that she is locked away somewhere, mainly because we haven’t found the body yet and we have only just started Katherine and Fredrick’s story line. Yet, I did see an interview that said the battle will come with casualties as we observed with Graham. So I’m really unsure. If Katherine didn’t have a heart i think it would have had to be taken out in FTL not SB. Taking out someone’s heart and allowing them to still be functional is definitely not something we can do in our world and as there has been no evidence of magic.
I also wondered if the dna sent in was tampered with. It would not be unheard of to, say, send in the heart of a horse with a strand of mane – it could easily be mistaken for hair and the DNA would come out a match.
All in all though, I unfortunately think she may have not slipped through Ragina’s hands. She has made it clear to us that she disposes of those she no longer has a need for. David loves MM and Katherine saw that. She can no longer be used as a puppet to keep them apart and therefore has no use to the EQ.