Short answer: if you want to join because you want to work with your pup and learn and have fun, and the club is okay with that, then I would go ahead and join. I think they just didn't want you to get your hopes up and then get disappointed later on, although they could have communicated this to you in a more tactful, less insensitive way.
Experienced Schutzhund people can tell a lot about a pup just by observing. If you can see the difference in drive between your pup and the other members pups, then they can see even more differences. Not to say that with work and dedication your pup can't do the work, but it will be more work and it can be very frustrating to see other people's dogs progress when you are working twice as hard with your own dog to get half the results. And I'm talking from experience - I started schutzhund with my mixed breed, so had some great ability in some areas, not so much in others, and I certainly was working twice as hard with her as I am with my present working line. But it was fun, we both enjoyed it, I learned a lot, she improved tremendously (our helper could not believe how much she improved, yet we still cannot get out of her what comes to the more driven dogs more naturally), we got some (minor) titles, I got hooked on Schutzhund and training in general, and got immense satisfaction from the whole process, frustrations and disappointments and all, and wouldn't hesitate to do it all over again if I were a clueless newbie all over again.
Where your pup comes from and what titles her parents have, and what allergies she had to deal with prior to starting training has no effect right now. The pup in front of you will show you if she is up to the training or not. It sounds to me like the club was being honest (again, a bit insensitive though).
So if you like the people, and want to learn, and want to see how far you can go with your girl, and the club is open to working with you, then I would express your thoughts and wishes and continue on, if the money is not an issue for you.
Your girl may surprise you and everyone else, and not make excuses for her, I think it can be a great experience