Supergirl and clones? Religion and the soul? Hmm...
I'm not sure there's much on Supergirl that could be used for such a topic, at least not the Pre-Crisis version. Checking DarkMark's excellent comics indexing domain, I found two incidents when the "classic" Kara Zor-El was cloned, but religious aspects weren't really discussed.
"Supergirl" v.1 #10 (Sept-Oct 1974) had as a backstory "Her Brother's Keeper", where geneticist Dr. Forte creates a "SuperLAD" from a secretly-retrieved Supergirl cell sample. After Supergirl discovers her "twin brother" robbing banks for Forte, the clone questions Forte on why he was raised without a sense of morality. Superlad later proves he has an ethical conscience when he kills himself rather than execute the captured Supergirl. Now, it's not feasible to create a male clone from only female genetic material, so the science is off in this story. Besides, most Supergirl fans consider her first solo series rather lacking in writing quality -- it only lasted TEN issues.
"The Daring New Adventures of Supergirl" #10 (August 1983) began a four-issue story (in Issue #13 the title was shortened to just "Supergirl", thus it's considered her second series) where Professor Drake creates six 12-inch-tall Supergirl clones. Needless to say, the scientific logic behind six Super-Barbie dolls battling Supergirl is inexplicable. But wait until you see...
"Supergirl" v.2 #19. The defeated and permanently depowered mini-clones merge into one full-sized adult and escape! Not only that, but somehow the combined clone forgets her original nature and believes she's Supergirl who mysteriously lost her powers. In the meantime the real Supergirl forgets her civilian identity as Linda Danvers, so we have the clone masquerading as Linda and wondering who this super-impostor is while the real Supergirl wonders what she's supposed to do when "off duty". Eventually the real Supergirl and her clone recover their memories and strike a deal -- Supergirl will find a NEW identity for her clone to live a normal life as she now desires. Sadly, we never had a follow-up on this tale, since "Supergirl" was suddenly cancelled at #23, and Kara herself died during the Crisis on Infinite Earths a year after that.
The Post-Crisis Supergirl was Matrix, who was actually an artificial genetic lifeform. (Not QUITE a clone, but close enough?) Her shape-changing protoplasm was cloned in the "Supergirl" mini-series (volume 3), but an outraged "Mae" destroyed them.
Being an artificial being, Matrix did question what it meant to be "human". This was further explored (with a LOT of religious overtones) during Peter David's 80-issues series ("Supergirl", v.4). You should consult
http://supergirl.astraldream.net/ for more details on this series -- this series probably has more relevance to your study.
Recently there was also a "partial" female clone of Superman. Posing as Clark and Lois' future daughter, Cir-El was actually a brainwashed human girl who was genetically modified with Superman's DNA extracted from a hair sample. Poorly received by Supergirl fans, Cir-El "erased herself" by jumping into a Timestream and presumably preventing her own creation. I think you can mostly ignore this one. ;-)
Good luck with your project.