TBH I don't think Utena actually knows what to do with Kiwi's very openly expressed crush. It's arguably an aspect of the gulf between her supervillain and civilian personas (and conversely the fact Dumplings simply doesn't compartementalize between the two); as Magia Baiser the BDSM Dark Magical Girl she'll gleefully and confidently go full hentai doujin on (almost) anybody anytime, but as Hiiragi Utena the awkward 14-year old girl she's completely at a loss how to cope with someone expressing romantic-sexual interest in her.
Bit of a glass cannon in other words - she can dish it out but not take it. :P
(The peculiarly familial relationship the two of them have with Korisu probably only confuses her further in this regard.)
It's possible that Kiwi (with rather uncharacteristic sensitivity) realizes this to some degree, too, as while she's not at all subtle about her raging homo lust for Utena she never really presses the issue. It's more like she's extending a permanent open invitation (and rather vocally at that) but is fine with waiting for an answer.