Ask a Lawyer and Get Answers to Your Legal Questions
Most railroad crossings (even inactive ones) are covered by Federal Law. You will want to contact the railroad that owns the crossing (it may not be the same rail company that is running trains on the track (or was last running trains on the track), so this may take a little bit of research - a local title company can usually assist you with this.
Once you have identified the railroad easement you can better identify what entity you need to negotiate with and how best to proceed.
If the County is acting "arbitrarily or capriciously" (meaning they singled out your church for an improper purpose) you may have a civil claim against the county.
Unfortunately bringing civil lawsuits against county agencies for their legislative actions is notoriously difficult (courts do not want to get involved in legislative discretion (the "separation of powers" issue), and only do so if there is a clear violation of powers, such as a county council that is abusing its power or position.
If you think that the council is doing something like this, I would recommend hiring a local attorney, the best way to attack this type of thing is to act aggressively early (before it goes to a vote) and try to stop it in the administrative/legislative phase. If you wait until after they have made a decision, you can still fight them, but if you are in litigation, it gets very expensive (usually outside the scope of what most church groups are going to be interested in spending), and very time consuming - civil litigation like this can take 3-5 years.