What I'd do if I were you is try and find a third party - you are very close to and passionate about this (a good thing!), but she's a careing, thinking, feeling human being and must have reasons that need to be addressed - it can't be spite. I'd look for someone to mediate discussions (your pastor seems to be acting in this role already to a certain extent), not necessarily to set up a compromise, but to make sure that everyone is heard and not hurt during the discussion.
The second thing I'd do (maybe at the same time) is start a pettition. I'd sign it, but she, and the church, rightly wouldn't care about my signature. They'd care about the pastor's. They'd care about their neighbors' sigs, other members' sigs, anybody. Maybe if you line up a decent majority of the members, your cause no longer belongs to a perceived "vocal minority".
I'd also get it in writing - even an email - from someone at PennDOT that a permit isn't necessary. This being unofficial might make that difficult. If that's impossible, I'd try to get the permit. Even if it's not required - if you have one or proof you don't need one, that is no longer a valid part of their argument against it.
Armed with an attempted mediation (which may work), a pettition, and a permit (or proof you don't need it), the arguments on the other side, if they truly are as presented, no longer hold water and any insistence really says more about the opposers than the ghost bike. Only after that would I look for another permanent site. I see no reason not to set up a temporary site, or permanent one, if the other property owners on those corners are willing.
Best of luck.