"a church tower like that one over there with the gold ball on top"
St. Peter's Church (Peterskirche), Frankfurt am Main (before 1891)
Public DomainSt. Peter's Church (Peterskirche), Frankfurt am Main (before 1891) - Credit: unknown
St. Peter's Church, Frankfurt am Main, as it is today
GNU Free Documentation LicenseSt. Peter's Church, Frankfurt am Main, as it is today - Credit: Roland Meinecke

If you click on this link, you can see a list of churches which existed in Frankfurt before the two world wars.

Amongst those with high towers are St. Bartholomew's cathedral; the Church of the Magi; St. Katherine's Church; St. Paul's Church; and St. Peter's Church.

Perhaps the church mentioned in Heidi was St. Peter's. In the picture on the left, it is possible to see a small ball on the top of the tower (but not possible to see whether it is gold!). St. Peter's church was rebuilt in 1895.