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I think Homura doesn't feel affectionate towards Madoka, more conflicted and guilty. Because she might be willing to let her, at the least, be killed by witches instead of helping her.
Homura knows that Madoka is a kind and nice girl and possibly insane powerful. Somehow Homura is convinced that Madoka will end up as a witch (see beginning of episode one) and is trying to dissuade her from getting in contact with that part of the world.
First try was to prevent QB from getting in contact with her and would have been the best choice because Madoka just can't help but meddle. If she continues to do so, she would sooner or later cave in and make a contract (due to the danger to meddle with witches without any powers) and possibly make a bad wish or break under the demands of the job and, whatever is possible, become a witch.
So Homuras choices now are to let her die or kill her herself. My impression from the end of episode 4 is she is not pleased, maybe by Sayaka's choice, maybe not.
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