Generally speaking, what is governed by federal law and deemed actionable is discrimination in housing, employment, and employment practices (such as pay, benefits, schedules, types of assignments, breaks, training, promotions, etc.) The protected categories are race, gender, age, pregnancy, religion, national origin, disability, or genetic information. Even though religion is a protected class, this is not applicable in what you propose. (I'm not an attorney, but I spent the majority of my career working in HR.) The EEOC does not govern small employers who have less than 15 employees, and what you are proposing is not an employment practice. Of course, actionable discrimination can be considered for other issues than employment...public businesses, like a restaurant for example, can't say "we won't serve blacks" or hotels can't say "we won't rent a room to a Arab." Businesses can (and do) give discounts to seniors, veterans, etc. Your intent to give a discount to Christians is not discriminatory, since you are not discriminating AGAINST a protected class.
There have been examples of small businesses that have refused to service or sell to certain groups...for example, recently there was a gun shop that got some publicity for stating and advertising that it would not sell a gun to anyone who voted for Obama. Political affiliation is not a protected class, and the gun shop was not sufficiently large to come under EEOC regulation, so unless there is some state or local law preventing a small business owner from determining how he wants to conduct his business, it is not technically or legally discrimination, and the business owner is well within his rights under current law to do as he was doing.
As an individual contractor, you should be free to set your prices, unless some local or state regulation governs what you can charge (doubtful.) I don't think you will have any problem as long as you state a price up front that applies to everyone equally, and then reduce it for certain customers to whom you wish to give a discount, such as Christians or veterans, etc.