Several reasons I told her to leave me. There are the logical ones, perhaps the least important to me. Noise is an issue. It's ammunition when she's probably not that loaded with bullets.
More than that... this entire time, I've been trying to get Clem out of the crud alive this whole time, but also sane and as a 'good' person. I've never had her kill a living man, and I've tried not to kill them. As Lee says when you choose not to have her shoot you, you have to be careful with violence because it changes you. I don't want it to change her so much, only just so much as it has to for her to survive.
This is the same reason that I was hoping Omid and Christa would take care of her. Between them, they seemed like they could survive and still stay 'decent' as people.
Do I want Lee to become a walker? Hell no. But more than I don't want him to become a walker, I don't want Clem to become a monster in order to survive and I don't want her learning that she has to kill loved ones BEFORE they turn. So I see it as my last sacrifice as Lee, the final gift I can give even in that messed up, paralyzed state.
Hopefully it kept her just a little less changed by violence.
I never really even considered having her shoot me as an option. We call that 'strength' and in a zombie apocalypse it sort of is, but on a greater scale I call it horrifying, and it's in that greater scale that I hope she gets to live some day and that I prepare her for.
"Deserves it? I daresay he does. Many that live deserve death. Some that die deserve life. Can you give it to them? Then do not be too eager to deal out death in judgement. For even the very wise cannot see all ends."