Last year I published a religious book with a local publisher. It has a very finite audience and will probably sell 1,000 to 1,500 copies a year. If you google me, this book comes up on Amazon. My question is this: I am now writing thriller fiction; will this pigeonhole me to agents and make it harder for me to acquire one? I have no desire to publish anymore in the nonfiction religious genre as I saw a need and filled it.
It shouldn't pigeonhole you. When I read a query for a thriller the first thing I consider is the story. The second is whether I think there's a market. The third is whether the author is an asshat. Only then do I start looking at previous publication outside the genre.
It helps that you've been published in non-fiction, rather than fiction. Being a "debut novelist" is an easier sell than "novelist being resuscitated from the dead."