If you go into any business harboring that level of disrespect for your customers then you're probably going to fail to provide a product they'll be willing to use. Although there is also an argument to be made for domain experience - if you're going to sell a service to religious groups wouldn't you be more likely to understand the market without having a bias against religion?
On the other hand, if you're emotionally invested in atheism, in the sense that you actively want to see religion gone (as opposed to just not believing as a personal choice), you're emotionally invested in religion by extension.
I know a large number of religious people who would consider themselves "emotionally invested in their religion" but I would never describe any of them as "actively wanting to see all other beliefs gone".
"New Atheism is a social and political movement in favour of atheism and secularism promoted by a collection of modern atheist writers who have advocated the view that "religion should not simply be tolerated but should be countered, criticized, and exposed by rational argument wherever its influence arises.""
The code has been licensed under an Affero GPL v3 license so anybody using it in production must release any modifications done. So it's not really stealing the idea or the code, only the business model, which the OP apparently doesn't want to pursue anyway.
A non Affero license (or MIT, BSD, Apache) would have shut him off from his code (I can't decide if those using those licenses are masochists or just extremely kind). With this choice of the license the OP will get fixes and improvements and probably be happy with that. Furthermore he could be hired to do them, regardless of the license.