It sounds like she does love you, but the words are not coming from her.
If possible I would suggest making a trip up there on a weekend and taking her out for a meal to discuss it. A phone call or a letter is too easy to ignore.
Ask her specifically what about the visits she feels puts her in spiritual jeopardy and let her know that is not your intent at all and that you are willing to make changes for her. Would it be dropping her off at meetings while she visits? In service? Is it comments you inadvertantly make? Try to get her to explain it. "spiritual jeopardy" is an easy Witness term to drop and unlikely her own. Trying to get her to explain may give you better insight into why.
Also keep in mind that there may be a boy she likes in the congregation and being away for half the summer would keep her away. The spiritual issue could just be cover for teenage hormones.
At very least you will be a father who loves his daughter and is willing to meet her half way. Let her know that you are willing to work with her and while you will respect her wishes not to come, you will not give up on being her father and try to plan other visits like that one. At some point she is going to need a non-Witness shoulder to lean on and will know yours is available.