Theory #1:
My thought on the ending was Lena is not a clone but the shimmer changed her. Whatever the shimmer was doing there, was not specifically to clone. It didnt clone anything but Kane. EVERYTHING else, both plants and animals werent cloned, they were changed. Lena absorbed the shimmer in my opinion. The clone that was created first did in fact die. It being a clone of Lena is what allowed Lena to kill it. Because the clone also has her destructive nature. But the change in Lena was already complete regardless of the fate of the clone at that point. Lena 2.0 killed the shimmer clone.
Theory #2:
The initial opinion I had was that after being knocked unconscious, the positions were switched. Now what we see as the clone, is the real Lena and Lena we see is the clone. So the clone wasnt keeping Lena from leaving the lighthouse, it was the real Lena keeping the clone from leaving. The clones dont have superhuman strength or anything and the real Lena had military training that the clone couldnt mimic. Hence why she was able to knock the clone out after it tried to grab the tripod. Now the real Lena is already aware that her husband is dead. The real him. She is also aware that her DNA is changing to a point where she will not survive. At this point there is nothing for her to live for honestly. The clone, knowing how self destructive she is, hands real Lena the grenade. Lena being destructive in nature, does not fight the clone pulling the pin. She is accepting it like her real husband did. Real Lena died.