Based on this, I think Kagami doesn't have her feelings yet sorted for Indou. C'mon Kagami, be more honest with yourself!
Oh, I think she's honest enough with herself, just not with Indou. She simply seems to want a real relationship free of the implications of the Maiden system.
And that Maiden System is still a bit blurry to me. The “chigo” discussion helped a little (and sorry if I was misunderstanding the implications of the word), but it’s still not clear if it’s a “senior’s pet + kissing” thing, or something more sexual, or what, exactly.
Blurry it is, yes. Based on the discussion, it's likely a similar meaning to the original samurai use, but without an actual in-series explanation it's difficult to tell. Still, Kagami has made it rather clear from the start that she does not like the Maiden system and does not want one, while also wanting to protect Indou from becoming one. Any feelings she has for Indou that have led to kissing her, she has developed without regard for this, which is also causing these problems in their relationship - as Indou is even more lost than we regarding what Maidens are supposed to be, she is taking Kagami's denial of her Maiden status as denying their relationship as a whole, while Kagami herself seems afraid of taking things further, thinking it would be seen as a confirmation of her seeing Indou as "just a Maiden".