Darn, Marisa is really getting put through the wringer in this doujin. One challenge after another and now, while she's at her lowest, Okina steps in for some more abuse.
Pretty sure the danger is not Reimu "having to kill" Marisa when she turns. As I see it, this rule applies more to existing villagers breaking out of the system, which Marisa hasn't been a part of in a long time.
As I see it, the danger is the big rift between Reimu and Marisa that would be created. After all, Marisa turning would put her in a place that "Reimu's hand can't reach" as described prior. The hakurei shrine maiden's job is kind of doomed to solitude in a certain way, a human that acts as a single intermediary between humans and youkai and as such doesn't belong to either. She can befriend either of course, but there will always distance between her and anyone else in terms of the "world" they live in.
Fortunately, we have Marisa at Reimu's side in a very similar position, a human that doesn't belong to either group and as such, has always been at her side to keep her company. Engage with her on the same level both as a rival and a very close friend.
Of course, if Marisa were to become a youkai, those two would still likely be friends, Marisa is still Marisa after all, but not "close" friends anymore and for sure not romantically.